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1

USC study finds unique genetic marker may improve detection of recurrent ovarian cancer:  

Cancer.gov

Ovarian cancer is a major health concern for women and the identification of sensitive biomarkers for early detection and/or monitoring of disease recurrence is of high clinical relevance. New work published in the Dec. 7 issue of the online journal PLoS ONE reports promising advances toward the development of blood-based DNA markers for ovarian cancer.

2

Genetic Markers Unique to Listeria monocytogenes Serotype 4b Differentiate Epidemic Clone II (Hot Dog Outbreak Strains) from Other Lineages  

PubMed Central

A small number of closely related strains of Listeria monocytogenes serotype 4b, designated epidemic clone I (ECI), have been implicated in numerous outbreaks of food-borne listeriosis described during the past two decades in Europe and North America. In 1998 to 1999, a multistate outbreak traced to contaminated hot dogs involved a different strain type of serotype 4b, with genetic fingerprints rarely encountered before. In spite of the profound economic and public health impact of this outbreak, the implicated bacteria (designated epidemic clone II [ECII]) have remained poorly characterized genetically, and nucleotide sequences specific for these strains have not been reported. Using genome sequence information, PCR, and Southern blots, we identified DNA fragments which appeared to be either absent or markedly divergent in the hot dog outbreak strains but conserved among other serotype 4b strains. PCR with primers derived from these fragments as well as Southern blots with the amplicons as probes readily differentiated ECII from other serotype 4b strains. The serotype 4b-specific region harboring these fragments was adjacent to inlA, which encodes a well-characterized virulence determinant. The findings suggest that ECII strains have undergone divergence in portions of a serotype-specific region that is conserved in other serotype 4b strains. Although the mechanisms that drive this divergence remain to be identified, DNA-based tools from this region can facilitate the detection and further characterization of strains belonging to this lineage.

Evans, Matthew R.; Swaminathan, Bala; Graves, Lewis M.; Altermann, Eric; Klaenhammer, Todd R.; Fink, Ryan C.; Kernodle, Sheri; Kathariou, Sophia

2004-01-01

3

Genetic markers unique to Listeria monocytogenes serotype 4b differentiate epidemic clone II (hot dog outbreak strains) from other lineages.  

PubMed

A small number of closely related strains of Listeria monocytogenes serotype 4b, designated epidemic clone I (ECI), have been implicated in numerous outbreaks of food-borne listeriosis described during the past two decades in Europe and North America. In 1998 to 1999, a multistate outbreak traced to contaminated hot dogs involved a different strain type of serotype 4b, with genetic fingerprints rarely encountered before. In spite of the profound economic and public health impact of this outbreak, the implicated bacteria (designated epidemic clone II [ECII]) have remained poorly characterized genetically, and nucleotide sequences specific for these strains have not been reported. Using genome sequence information, PCR, and Southern blots, we identified DNA fragments which appeared to be either absent or markedly divergent in the hot dog outbreak strains but conserved among other serotype 4b strains. PCR with primers derived from these fragments as well as Southern blots with the amplicons as probes readily differentiated ECII from other serotype 4b strains. The serotype 4b-specific region harboring these fragments was adjacent to inlA, which encodes a well-characterized virulence determinant. The findings suggest that ECII strains have undergone divergence in portions of a serotype-specific region that is conserved in other serotype 4b strains. Although the mechanisms that drive this divergence remain to be identified, DNA-based tools from this region can facilitate the detection and further characterization of strains belonging to this lineage. PMID:15066835

Evans, Matthew R; Swaminathan, Bala; Graves, Lewis M; Altermann, Eric; Klaenhammer, Todd R; Fink, Ryan C; Kernodle, Sheri; Kathariou, Sophia

2004-04-01

4

Unique among unique. Is it genetically determined?  

PubMed

The cross-country world championship is one of the best models to study characteristics needed to achieve top-level endurance athletic capacity. We report the genotype combination of a recent cross-country champion (12 km race) in polymorphisms of seven genes that are candidates to influence endurance phenotype traits (ACTN3, ACE, PPARGC1A, AMPD1, CKMM, GDF8 (myostatin) and HFE). His data were compared with those of eight other runners (world-class but not world champions). The only athlete with the genotype theoretically more suited to attaining world-class endurance running performance was the case study subject. A favourable genetic endowment, together with exceptional environmental factors (years of altitude living and training in this case), seems to be necessary to attain the highest possible level of running endurance performance. PMID:18662936

Gonzalez-Freire, M; Santiago, C; Verde, Z; Lao, J I; Oiivan, J; Gómez-Gallego, F; Lucia, A

2009-04-01

5

Genetic markers in Welsh gypsies.  

PubMed Central

Data are presented on polymorphic genetic markers of 84 Welsh gypsies, members of an inbred population characterised by a high incidence of phenylketonuria and other recessively inherited diseases. Sixteen polymorphic loci were studied: the ABO blood group distribution was comparable to that of the surrounding population, the B gene frequency being 7-5%, a lower frequency than most earlier studies in gypsies. The haptoglobin 1 gene frequency (23-7%) was very different from that of the British population, resembling the frequency found in India and some previously reported gypsy groups. The data on Welsh gypsies for the various loci are discussed in relation to the known evidence for a number of European gypsy populations, and in relation to the genetic structure of these populations. It is concluded that genetic divergence has occurred in the European gypsies, and that this may have been accentuated by the dispersal, isolation, and inbreeding which have occurred during the present century.

Harper, P S; Williams, E M; Sunderland, E

1977-01-01

6

DNA marker technologies and their applications in aquaculture genetics  

Microsoft Academic Search

The development of DNA-based genetic markers has had a revolutionary impact on animal genetics. With DNA markers, it is theoretically possible to observe and exploit genetic variation in the entire genome. Popular genetic markers in the aquaculture community include allozymes, mitochondrial DNA, RFLP, RAPD, AFLP, microsatellite, SNP, and EST markers. The application of DNA markers has allowed rapid progress in

Z. J. Liu; J. F. Cordes

2004-01-01

7

Mapping the Human Genome With Genetic Markers.  

National Technical Information Service (NTIS)

Dr. Donis-Keller describes the use of restriction fragment polymorphisms (RFLPS) as genetic markers for assigning the location of individual genes on a chromosome. This approach has been used in the analysis of such human diseases as Huntington's disease,...

1994-01-01

8

Zebrafish Genetic Map with 2000 Microsatellite Markers  

Microsoft Academic Search

The zebrafish is the first vertebrate organism used for large-scale genetic screens seeking genes critical to development. These screens have been quite successful, with more than 1800 recessive mutations discovered that speak to morphogenesis of the vertebrate embryo. The cloning of the mutant genes depends on a dense genetic map. The 2000 markers we present here, using microsatellite (CA) repeats,

Nobuyoshi Shimoda; Ela W. Knapik; John Ziniti; Chäng Sim; Erika Yamada; Stacy Kaplan; Donald Jackson; Frederic de Sauvage; Howard Jacob; Mark C. Fishman

1999-01-01

9

Genetic markers on chromosome 7.  

PubMed Central

Chromosome 7 is frequently associated with chromosome aberrations, rearrangements, and deletions. It also contains many important genes, gene families, and disease loci. This brief review attempts to summarise these and other interesting aspects of chromosome 7. With the rapid accumulation of cloned genes and polymorphic DNA fragments, this chromosome has become an excellent substrate for molecular genetic studies.

Tsui, L C

1988-01-01

10

Microsatellite markers reveal genetic differentiation among populations of Sclerotinia sclerotiorum from Australian canola fields  

Microsoft Academic Search

Eight microsatellite markers were applied to 154 Sclerotinia sclerotiorum isolates from four Australian canola fields, to determine the extent of genetic variation and differentiation in populations of this pathogen. A total of 82 different haplotypes were identified and in each population many haplotypes were unique. Mycelial compatibility grouping, a phenotypic marker system controlled by multiple loci, was often associated with

Adrienne C. Sexton; Barbara J. Howlett

2004-01-01

11

The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers.  

PubMed

With an objective to develop a genetic map in pigeon pea (Cajanus spp.), a total of 554 diversity arrays technology (DArT) markers showed polymorphism in a pigeon pea F(2) mapping population of 72 progenies derived from an interspecific cross of ICP 28 (Cajanus cajan) and ICPW 94 (Cajanus scarabaeoides). Approximately 13% of markers did not conform to expected segregation ratio. The total number of DArT marker loci segregating in Mendelian manner was 405 with 73.1% (P > 0.001) of DArT markers having unique segregation patterns. Two groups of genetic maps were generated using DArT markers. While the maternal genetic linkage map had 122 unique DArT maternal marker loci, the paternal genetic linkage map has a total of 172 unique DArT paternal marker loci. The length of these two maps covered 270.0 cM and 451.6 cM, respectively. These are the first genetic linkage maps developed for pigeon pea, and this is the first report of genetic mapping in any grain legume using diversity arrays technology. PMID:21677394

Yang, Shi Ying; Saxena, Rachit K; Kulwal, Pawan L; Ash, Gavin J; Dubey, Anuja; Harper, John D I; Upadhyaya, Hari D; Gothalwal, Ragini; Kilian, Andrzej; Varshney, Rajeev K

2011-04-01

12

Genetic and biological markers in drug abuse and alcoholism  

SciTech Connect

This book contains 11 selections. Some of the titles are: Polymorphic Gene Marker Studies; Pharmacogenetic Approaches to the Prediction of Drug Response; Genetic Markers of Drug Abuse in Mouse Models; Genetics as a Tool for Identifying Biological Markers of Drug Abuse; and Studies of an Animal Model of Alcoholism.

Braude, M.C.; Chao, H.M.

1986-01-01

13

Intelligence and genetic markers in Chilean children.  

PubMed

Genetic markers and total intelligence quotient (IQ) assessed by WISC (Wechsler Intelligence Scale for Children) were studied in children of both sexes from Santiago, Chile. Heterozygous boys for phosphoglucomutase 1 (PGM) and heterozygous girls for haptoglobin (Hp) had lower IQ than homozygotes. For ABO system, B girls had lower and B boys had higher IQ than children with other ABO phenotypes. These differences were highly significant with the two tailed t'-test (Student's t-test with the Welch-Satterthwaite correction for degrees of freedom), and most of them remained significant after the correction for multiple comparisons. Girls had greater variance of IQ than boys. Relationships between homozygotes and heterozygotes were found in two independent studies. Thus, the genetic relationship found here seems likely to be a true biotic effect. PMID:10347742

Valenzuela, C Y; Pastene, C S; Pérez, C M

1998-01-01

14

Modeling the Genetic Architecture of Complex Traits With Molecular Markers  

Microsoft Academic Search

Understanding the genetic control of quantitatively inherited traits is fundamental to agricultural, evolutionary and biomedical genetic research. A detailed picture of the genetic architecture of quantitative traits can be elucidated with a well-saturated genetic map of molecular markers. The parameters that quantify the genetic architecture of a trait include the number of individual quantitative trait loci (QTL), their genomic positions,

Rongling Wu; Wei Hou; Yuehua Cui; Hongying Li; Tian Liu; Song Wu; Chang-Xing Ma; Yanru Zeng

2007-01-01

15

Genetic Traceability of Black Pig Meats Using Microsatellite Markers  

PubMed Central

Pork from Jeju black pig (population J) and Berkshire (population B) has a unique market share in Korea because of their high meat quality. Due to the high demand of this pork, traceability of the pork to its origin is becoming an important part of the consumer demand. To examine the feasibility of such a system, we aim to provide basic genetic information of the two black pig populations and assess the possibility of genetically distinguishing between the two breeds. Muscle samples were collected from slaughter houses in Jeju Island and Namwon, Chonbuk province, Korea, for populations J and B, respectively. In total 800 Jeju black pigs and 351 Berkshires were genotyped at thirteen microsatellite (MS) markers. Analyses on the genetic diversity of the two populations were carried out in the programs MS toolkit and FSTAT. The population structure of the two breeds was determined by a Bayesian clustering method implemented in structure and by a phylogenetic analysis in Phylip. Population J exhibited higher mean number of alleles, expected heterozygosity and observed heterozygosity value, and polymorphism information content, compared to population B. The FIS values of population J and population B were 0.03 and ?0.005, respectively, indicating that little or no inbreeding has occurred. In addition, genetic structure analysis revealed the possibility of gene flow from population B to population J. The expected probability of identify value of the 13 MS markers was 9.87×10?14 in population J, 3.17×10?9 in population B, and 1.03×10?12 in the two populations. The results of this study are useful in distinguishing between the two black pig breeds and can be used as a foundation for further development of DNA markers.

Oh, Jae-Don; Song, Ki-Duk; Seo, Joo-Hee; Kim, Duk-Kyung; Kim, Sung-Hoon; Seo, Kang-Seok; Lim, Hyun-Tae; Lee, Jae-Bong; Park, Hwa-Chun; Ryu, Youn-Chul; Kang, Min-Soo; Cho, Seoae; Kim, Eui-Soo; Choe, Ho-Sung; Kong, Hong-Sik; Lee, Hak-Kyo

2014-01-01

16

Genetic uniqueness of the Waorani tribe from the Ecuadorian Amazon  

PubMed Central

South America and especially the Amazon basin is known to be home to some of the most isolated human groups in the world. Here, we report on a study of mitochondrial DNA (mtDNA) in the Waorani from Ecuador, probably the most warlike human population known to date. Seeking to look in more depth at the characterization of the genetic diversity of this Native American tribe, molecular markers from the X and Y chromosomes were also analyzed. Only three different mtDNA haplotypes were detected among the Waorani sample. One of them, assigned to Native American haplogroup A2, accounted for more than 94% of the total diversity of the maternal gene pool. Our results for sex chromosome molecular markers failed to find close genetic kinship between individuals, further emphasizing the low genetic diversity of the mtDNA. Bearing in mind the results obtained for both the analysis of the mtDNA control region and complete mitochondrial genomes, we suggest the existence of a ‘Waorani-specific' mtDNA lineage. According to current knowledge on the phylogeny of haplogroup A2, we propose that this lineage could be designated as subhaplogroup A2s. Its wide predominance among the Waorani people might have been conditioned by severe genetic drift episodes resulting from founding events, long-term isolation and a traditionally small population size most likely associated with the striking ethnography of this Amazonian community. In all, the Waorani constitute a fine example of how genetic imprint may mirror ethnopsychology and sociocultural features in human populations.

Cardoso, S; Alfonso-Sanchez, M A; Valverde, L; Sanchez, D; Zarrabeitia, M T; Odriozola, A; Martinez-Jarreta, B; de Pancorbo, M M

2012-01-01

17

High-definition genome profiling for genetic marker discovery  

Microsoft Academic Search

Genetic mapping is a key step towards isolating genes and genetic markers associated with phenotypic traits by elucidating their genetic positions. The success of this approach depends on precision in pinpointing genetic positions and the effectiveness of the discovery process. Recent advances in microarray technology and the increasing availability of genomic information have provided an opportunity to use microarrays to

Tong Zhu; John Salmeron

2007-01-01

18

Using surface-enhanced Raman spectroscopy to probe for genetic markers on single-stranded DNA  

NASA Astrophysics Data System (ADS)

Methods capable of quickly and inexpensively collecting genetic information are of increasing importance. We report a method of using surface-enhanced Raman spectroscopy to probe single-stranded DNA for genetic markers. This unique approach is used to analyze unmodified genes of moderate length for genetic markers by hybridizing native test oligonucleotides into a surface-enhanced Raman complex, vastly increasing detection sensitivity as compared to traditional Raman spectroscopy. The Raman complex is formed by sandwiching the test DNA between 40-nm gold nanoparticles and a photolithographically defined gold surface. With this design, we are able to collect characteristic Raman spectra about the test DNA and to detect genetic markers such as single-nucleotide polymorphisms (SNPs) and polymorphic regions. Results show that strands containing one of three different types of polymorphism can be differentiated using statistically significant trends regarding Raman intensity.

Moody, Benjamin; Leotaud, John; McCarty, Gregory S.

2010-03-01

19

Uniquely human evolution of sialic acid genetics and biology  

PubMed Central

Darwinian evolution of humans from our common ancestors with nonhuman primates involved many gene–environment interactions at the population level, and the resulting human-specific genetic changes must contribute to the “Human Condition.” Recent data indicate that the biology of sialic acids (which directly involves less than 60 genes) shows more than 10 uniquely human genetic changes in comparison with our closest evolutionary relatives. Known outcomes are tissue-specific changes in abundant cell-surface glycans, changes in specificity and/or expression of multiple proteins that recognize these glycans, and novel pathogen regimes. Specific events include Alu-mediated inactivation of the CMAH gene, resulting in loss of synthesis of the Sia N-glycolylneuraminic acid (Neu5Gc) and increase in expression of the precursor N-acetylneuraminic acid (Neu5Ac); increased expression of ?2–6-linked Sias (likely because of changed expression of ST6GALI); and multiple changes in SIGLEC genes encoding Sia-recognizing Ig-like lectins (Siglecs). The last includes binding specificity changes (in Siglecs -5, -7, -9, -11, and -12); expression pattern changes (in Siglecs -1, -5, -6, and -11); gene conversion (SIGLEC11); and deletion or pseudogenization (SIGLEC13, SIGLEC14, and SIGLEC16). A nongenetic outcome of the CMAH mutation is human metabolic incorporation of foreign dietary Neu5Gc, in the face of circulating anti-Neu5Gc antibodies, generating a novel “xeno-auto-antigen” situation. Taken together, these data suggest that both the genes associated with Sia biology and the related impacts of the environment comprise a relative “hot spot” of genetic and physiological changes in human evolution, with implications for uniquely human features both in health and disease.

Varki, Ajit

2010-01-01

20

Usefulness of WRKY gene-derived markers for assessing genetic population structure: An example with Florida coconut cultivars  

Microsoft Academic Search

We previously analyzed genetic diversity and population structure of eight cultivars within Florida coconut (Cocos nucifera L.) germplasm using 15 microsatellite (simple sequence repeat, SSR) markers. Here we report on the analysis of the same genotypes using 13 markers derived from WRKY sequences containing single nucleotide polymorphisms (SNP) and one microsatellite. WRKY transcription factors are unique to plants and are

Margarita Mauro-Herrera; Alan W. Meerow; James W. Borrone; David N. Kuhn; Raymond J. Schnell

2007-01-01

21

USC researchers link genetic marker to rectal cancer treatment:  

Cancer.gov

A team of University of Southern California researchers has identified a genetic marker that may predict which patients with rectal cancer can be cured by certain chemotherapies when combined with surgery.

22

Isolation of Bacteroides from fish and human fecal samples for identification of unique molecular markers.  

PubMed

Bacteroides molecular markers have been used to identify human fecal contamination in natural waters, but recent work in our laboratory confirmed cross-amplification of several human-specific Bacteroides spp. assays with fecal DNA from fish. For identification of unique molecular markers, Bacteroides from human (n = 4) and fish (n = 7) fecal samples were cultured and their identities were further confirmed using Rapid ID 32A API strips. The 16S rDNA from multiple isolates from each sample was PCR amplified, cloned, and sequenced to identify unique markers for development of more stringent human-specific assays. In human feces, Bacteroides vulgatus was the dominant species (75% of isolates), whereas in tilapia feces, Bacteroides eggerthii was dominant (66%). Bacteroides from grass carp, channel catfish, and blue catfish may include Bacteroides uniformis, Bacteroides ovatus, or Bacteroides stercoris. Phylogenic analyses of the 16S rRNA gene sequences showed distinct Bacteroides groupings from each fish species, while human sequences clustered with known B. vulgatus. None of the fish isolates showed significant similarity to Bacteroides sequences currently deposited in NCBI (National Center for Biotechnology Information). This study expands the current sequence database of cultured fish Bacteroides. Such data are essential for identification of unique molecular markers in human Bacteroides that can be utilized in differentiating fish and human fecal contamination in water samples. PMID:24313449

Kabiri, Leila; Alum, Absar; Rock, Channah; McLain, Jean E; Abbaszadegan, Morteza

2013-12-01

23

Genetic Counseling Using BRCA1-Linked Markers.  

National Technical Information Service (NTIS)

Rapid developments in cancer genetics have exposed a knowledge vacuum about genetic testing for susceptibility to cancer. Our experience in testing for BRCA1 or BRCA2 mutation in hereditary breast cancer (HBC) syndrome, with counseling about cancer survei...

1997-01-01

24

Automation of genetic linkage analysis using florescent microsatellite markers  

Microsoft Academic Search

Automation of the typing of genetic markers offers advantages of speed, accuracy, and cost in the mapping of genetic traits and the construction of high-resolution linkage maps. The authors have developed an automated linkage analysis system by (i) using a robotic pipettor to set up polymerase chain reactions (PCR) to amplify microsatellites with incorporation of a single fluorescent label; (ii)

D. C. Mansfield; A. F. Brown; D. K. Green

1994-01-01

25

Toward Diagnostic and Phenotype Markers for Genetically Transmitted Speech Delay  

ERIC Educational Resources Information Center

Converging evidence supports the hypothesis that the most common subtype of childhood speech sound disorder (SSD) of currently unknown origin is genetically transmitted. We report the first findings toward a set of diagnostic markers to differentiate this proposed etiological subtype (provisionally termed "speech delay-genetic") from other…

Shriberg, Lawrence D.; Lewis, Barbara A.; Tomblin, J. Bruce; McSweeny, Jane L.; Karlsson, Heather B.; Scheer, Alison R.

2005-01-01

26

Genetic characterization of Barbari goats using microsatellite markers  

Microsoft Academic Search

Genetic variation in Barbari goats, a highly prolific breed distributed widely in the northern part of India, known for better milk and meat quality, was studied as a part of genetic characterization and conservation. The genomic DNA from 50 unrelated Barbari goats were amplified via PCR with a panel of 21 microsatellite markers, and resolved through 6 per cent denaturing

J. Ramamoorthi; K. Thilagam; S. N. Sivaselvam; S. M. K. Karthickeyan

2009-01-01

27

Beyond STRs: The Role of Diallelic Markers in Forensic Genetics.  

PubMed

Short tandem repeat (STR) polymorphisms have been firmly established as standard DNA marker systems since more than 15 years both in forensic stain typing as well as in paternity and kinship testing. However, when analyzing genetic relationships in deficiency cases, STRs have a couple of disadvantages due to the sometimes poor biostatistical efficiency as well as the possibility to observe one or more genetic inconsistencies that could also be explained by mutational events. In such situations, additional robust markers with negligible mutations rates such as single nucleotide polymorphisms (SNPs) and insertion/deletion markers (indels) can be used as adjuncts to provide decisive genetic information in favor for or against the assumed relationship. Both SNPs and indels can now be typed more easily using multiplexes of up to 50 loci based on fragment length analysis on instruments available in all routine forensic and paternity testing laboratories, thus making it possible to extend the range of markers beyond the currently used STRs. PMID:22851932

Schneider, Peter M

2012-06-01

28

Beyond STRs: The Role of Diallelic Markers in Forensic Genetics  

PubMed Central

Short tandem repeat (STR) polymorphisms have been firmly established as standard DNA marker systems since more than 15 years both in forensic stain typing as well as in paternity and kinship testing. However, when analyzing genetic relationships in deficiency cases, STRs have a couple of disadvantages due to the sometimes poor biostatistical efficiency as well as the possibility to observe one or more genetic inconsistencies that could also be explained by mutational events. In such situations, additional robust markers with negligible mutations rates such as single nucleotide polymorphisms (SNPs) and insertion/deletion markers (indels) can be used as adjuncts to provide decisive genetic information in favor for or against the assumed relationship. Both SNPs and indels can now be typed more easily using multiplexes of up to 50 loci based on fragment length analysis on instruments available in all routine forensic and paternity testing laboratories, thus making it possible to extend the range of markers beyond the currently used STRs.

Schneider, Peter M.

2012-01-01

29

Genetics and biological markers of risk for alcoholism.  

PubMed Central

Substantial scientific evidence has accumulated that both genetic and environmental factors predispose the development of alcoholism in certain individuals. Evidence has accumulated to indicate that alcoholism is a heterogeneous entity arising from multiple etiologies. The demonstrated role of genetics in increasing the risk of alcoholism has promoted the search for biological markers that could objectively identify individuals who are genetically predisposed to alcoholism. Identifying such markers could allow for early diagnosis, focused prevention, and differential and type-specific treatment of alcoholism. Promising markers have been provided by research in electrophysiology, endocrinology, and biochemistry. Recent advances in molecular genetics are offering prospects for direct analysis of the human genome to determine elements that provide predisposition to, and protection from, alcoholism. Recent advances in research and new knowledge gained by the alcoholism treatment community and the lay public are helping to diminish the societal damage caused by alcohol abuse and alcoholism and to change prevailing attitudes about them.

Tabakoff, B; Hoffman, P L

1988-01-01

30

Genetics and biological markers of risk for alcoholism.  

PubMed

Substantial scientific evidence has accumulated that both genetic and environmental factors predispose the development of alcoholism in certain individuals. Evidence has accumulated to indicate that alcoholism is a heterogeneous entity arising from multiple etiologies. The demonstrated role of genetics in increasing the risk of alcoholism has promoted the search for biological markers that could objectively identify individuals who are genetically predisposed to alcoholism. Identifying such markers could allow for early diagnosis, focused prevention, and differential and type-specific treatment of alcoholism. Promising markers have been provided by research in electrophysiology, endocrinology, and biochemistry. Recent advances in molecular genetics are offering prospects for direct analysis of the human genome to determine elements that provide predisposition to, and protection from, alcoholism. Recent advances in research and new knowledge gained by the alcoholism treatment community and the lay public are helping to diminish the societal damage caused by alcohol abuse and alcoholism and to change prevailing attitudes about them. PMID:3141966

Tabakoff, B; Hoffman, P L

1988-01-01

31

Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster  

SciTech Connect

For nearly a century, genetic analysis in Drosophila melanogaster has been a powerful tool for analyzing gene function, yet Drosophila lacks the molecular genetic mapping tools that have recently revolutionized human, mouse and plant genetics. Here, we describe the systematic characterization of a dense set of molecular markers in Drosophila using an STS-based physical map of the genome. We identify 474 biallelic markers in standard laboratory strains of Drosophila that the genome. The majority of these markers are single nucleotide polymorphisms (SNPs) and sequences for these variants are provided in an accessible format. The average density of the new markers is 1 marker per 225 kb on the autosomes and 1 marker per 1 Mb on the X chromosome. We include in this survey a set of P-element strains that provide additional utility for high-resolution mapping. We demonstrate one application of the new markers in a simple set of crosses to map a mutation in the hedgehog gene to an interval of <1 Mb. This new map resource significantly increases the efficiency and resolution of recombination mapping and will be of immediate value to the Drosophila research community.

Hoskins, Roger A.; Phan, Alexander C.; Naeemuddin, Mohammed; Mapa, Felipa A.; Ruddy, David A.; Ryan, Jessica J.; Young, Lynn M.; Wells, Trent; Kopczynski, Casey; Ellis, Michael C.

2001-04-16

32

Genetic Counseling Using BRCAl-Linked Markers.  

National Technical Information Service (NTIS)

Since the initiation of this study, we have provided 14 BRCA1 and 2 BRCA2 families with information sessions held at various geographic areas of the United States. These sessions included intensive education about the natural history, genetics, surveillan...

H. T. Lynch

1996-01-01

33

Genetic variability of introduced and local Spanish peach cultivars determined by SSR markers  

Microsoft Academic Search

A set of 94 peach cultivars including Spanish native peach and foreign commercial cultivars were analyzed using 15 SSR markers,\\u000a selected for their high level of polymorphism. The number of alleles obtained varied from two to 11 with an average of 6.73\\u000a giving 185 different genotypes. All the cultivars showed a unique genetic profile, each one using different genotypic combination

Mariem Bouhadida; María Ángeles Moreno; María José Gonzalo; José Manuel Alonso; Yolanda Gogorcena

2011-01-01

34

Microsatellite marker development, mapping and applications in rice genetics and breeding  

Microsoft Academic Search

Microsatellites are simple, tandemly repeated di- to tetra-nucleotide sequence motifs flanked by unique sequences. They are valuable as genetic markers because they are co-dominant, detect high levels of allelic diversity, and are easily and economically assayed by the polymerase chain reaction (PCR). Results from screening a rice genomic library suggest that there are an estimated 5700-10 000 microsatellites in rice,

Susan R. McCouch; Xiuli Chen; Olivier Panaud; Svetlana Temnykh; Yunbi Xu; Yong Gu Cho; Ning Huang; Takashige Ishii; Matthew Blair

1997-01-01

35

Integrated microsatellite markers suitable for genetic studies of cytokine genes.  

PubMed

A panel of 13 highly informative dinucleotide repeats which are genetic markers for 17 cytokine genes and receptors is described. The marker panel is designed for use in fluorescence based semi-automated genotyping, with primers designed and labelled such that all 13 markers can be analysed in a single lane of a gel. Cytokine and cytokine receptors have a potential role in many diseases and pathological processes. Evidence suggests that cytokine production in vivo is influenced by polymorphisms within regulatory sequences of these genes. Genetic investigation of disease genes often requires genotyping of very large numbers of individuals. This panel of markers will, therefore, provide a useful tool to those wishing to undertake family-based linkage analysis studies of cytokine genes or large-scale association studies. PMID:9632534

John, S; Korman, Y; Ollier, W; Worthington, J

1998-06-01

36

Genetic markers in atherosclerosis: a review.  

PubMed Central

There is a growing number of lipoprotein markers recognized by immunological, electrophoretic, and other biochemical methods, and a beginning has been made on studying their modes of inheritance and linkage relations. Suggestive but inconclusive evidence of a relation between the cerumen polymorphism and arteriosclerosis has been published. Associations of the ABO blood groups with cardiovascular disease and serum lipid levels have been established, but the exact relation to lipoproteins and atherosclerosis remains to be determined.

Morton, N E

1976-01-01

37

Genetic diversity studies of Kherigarh cattle based on microsatellite markers  

Microsoft Academic Search

We report a genetic diversity study of Kherigarh cattle, a utility draught-purpose breed of India, currently declining at\\u000a a startling rate, by use of microsatellite markers recommended by the Food and Agriculture Organization. Microsatellite genotypes\\u000a were derived, and allelic and genotypic frequencies, heterozygosities and gene diversity were estimated. A total of 131 alleles\\u000a were distinguished by the 21 microsatellite markers

A. K. Pandey; Rekha Sharma; Yatender Singh; B. B. Prakash; S. P. S. Ahlawat

2006-01-01

38

DNA marker applications to molecular genetics and genomics in tomato.  

PubMed

Tomato is an important crop and regarded as an experimental model of the Solanaceae family and of fruiting plants in general. To enhance breeding efficiency and advance the field of genetics, tomato has been subjected to DNA marker studies as one of the earliest targets in plants. The developed DNA markers have been applied to the construction of genetic linkage maps and the resultant maps have contributed to quantitative trait locus (QTL) and gene mappings for agronomically important traits, as well as to comparative genomics of Solanaceae. The recently released whole genome sequences of tomato enable us to develop large numbers of DNA markers comparatively easily, and even promote new genotyping methods without DNA markers. In addition, databases for genomes, DNA markers, genetic linkage maps and other omics data, e.g., transcriptome, proteome, metabolome and phenome information, will provide useful information for molecular breeding in tomatoes. The use of DNA marker technologies in conjunction with new breeding techniques will promise to advance tomato breeding. PMID:23641178

Shirasawa, Kenta; Hirakawa, Hideki

2013-03-01

39

Comparison of RFLP and RAPD markers to estimating genetic relationships within and among cruciferous species  

Microsoft Academic Search

Restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers are being used widely for evaluating genetic relationships of crop germplasm. Differences in the properties of these two markers could result in different estimates of genetic relationships among some accessions. Nuclear RFLP markers detected by genomic DNA and cDNA clones and RAPD markers were compared for evaluating genetic

C. E. Thormann; M. E. Ferreira; L. E. A. Camargo; J. G. Tivang; T. C. Osborn

1994-01-01

40

Uniparental genetic markers in South Amerindians  

PubMed Central

A comprehensive review of uniparental systems in South Amerindians was undertaken. Variability in the Y-chromosome haplogroups were assessed in 68 populations and 1,814 individuals whereas that of Y-STR markers was assessed in 29 populations and 590 subjects. Variability in the mitochondrial DNA (mtDNA) haplogroup was examined in 108 populations and 6,697 persons, and sequencing studies used either the complete mtDNA genome or the highly variable segments 1 and 2. The diversity of the markers made it difficult to establish a general picture of Y-chromosome variability in the populations studied. However, haplogroup Q1a3a* was almost always the most prevalent whereas Q1a3* occurred equally in all regions, which suggested its prevalence among the early colonizers. The STR allele frequencies were used to derive a possible ancient Native American Q-clade chromosome haplotype and five of six STR loci showed significant geographic variation. Geographic and linguistic factors moderately influenced the mtDNA distributions (6% and 7%, respectively) and mtDNA haplogroups A and D correlated positively and negatively, respectively, with latitude. The data analyzed here provide rich material for understanding the biological history of South Amerindians and can serve as a basis for comparative studies involving other types of data, such as cultural data.

Bisso-Machado, Rafael; Bortolini, Maria Catira; Salzano, Francisco Mauro

2012-01-01

41

INSL5 may be a unique marker of colorectal endocrine cells and neuroendocrine tumors  

SciTech Connect

Highlights: ? INSL5 is expressed in enteroendocrine cells along the colorectum. ? INSL5 is expressed increasingly from proximal colon to rectum. ? INSL5 co-localizes rarely with chromogranin A. ? All rectal neuroendocrine tumors examined expressed INSL5. -- Abstract: Insulin-like peptide 5 (INSL5) is a member of the insulin superfamily, and is a potent agonist for RXFP4. We have shown that INSL5 is expressed in enteroendocrine cells (EECs) along the colorectum with a gradient increase toward the rectum. RXFP4 is ubiquitously expressed along the digestive tract. INSL5-positive EECs have little immunoreactivity to chromogranin A (CgA) and might be a unique marker of colorectal EECs. CgA-positive EECs were distributed normally along the colorectum in INSL5 null mice, suggesting that INSL5 is not required for the development of CgA-positive EECs. Exogenous INSL5 did not affect the proliferation of human colon cancer cell lines, and chemically-induced colitis in INSL5 null mice did not show any significant changes in inflammation or mucosal healing compared to wild-type mice. In contrast, all of the rectal neuroendocrine tumors examined co-expressed INSL5 and RXFP4. INSL5 may be a unique marker of colorectal EECs, and INSL5–RXFP4 signaling might play a role in an autocrine/paracrine fashion in the colorectal epithelium and rectal neuroendocrine tumors.

Mashima, Hirosato, E-mail: hmashima1-tky@umin.ac.jp [Department of Gastroenterology, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543 (Japan)] [Department of Gastroenterology, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543 (Japan); Ohno, Hideki [Division of Advanced Medical Science, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 (Japan)] [Division of Advanced Medical Science, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 (Japan); Yamada, Yumi; Sakai, Toshitaka; Ohnishi, Hirohide [Department of Gastroenterology, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543 (Japan)] [Department of Gastroenterology, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543 (Japan)

2013-03-22

42

A polymorphic DNA marker genetically linked to Huntington's disease  

Microsoft Academic Search

Family studies show that the Huntington's disease gene is linked to a polymorphic DNA marker that maps to human chromosome 4. The chromosomal localization of the Huntington's disease gene is the first step in using recombinant DNA technology to identify the primary genetic defect in this disorder.

James F. Gusella; Nancy S. Wexler; P. Michael Conneally; Susan L. Naylor; Mary Anne Anderson; Rudolph E. Tanzi; Paul C. Watkins; Kathleen Ottina; Margaret R. Wallace; Alan Y. Sakaguchi; Anne B. Young; Ira Shoulson; Ernesto Bonilla; Joseph B. Martin

1983-01-01

43

Evaluation of algorithms used to order markers on genetic maps.  

PubMed

When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F(2) populations were randomly simulated with 100 and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results. PMID:19639011

Mollinari, M; Margarido, G R A; Vencovsky, R; Garcia, A A F

2009-12-01

44

[ISSR markers and their applications in plant genetics].  

PubMed

Recently, inter-simple sequence repeat (ISSR) markers have emerged as an alternative system with reliability and advantages of microsatellites (SSR). The technique involves amplification of genomic segments flanked by inversely oriented and closely spaced microsatellite sequences by a single primer or a pair of primers based on SSRs anchored 5' or 3' with 1-4 purine or pyramidine residues. The sequences of repeats and anchor nucleates are arbitrarily selected. Coupled with the separation of amplification products on a polyacrylamide or agarose gels,ISSR amplification can reveal a much larger number of fragments per primer than RAPD. It is concluded that ISSR technique provides a quick, reliable and highly informative system for DNA fingerprinting.ISSR markers are inherited in Mendelin mode and segregated as dominant markers. This technique has been widely used in the studies of cultivar identification, genetic mapping, gene tagging,genetic diversity, evolution and molecular ecology. PMID:16135460

Wang, Jian-bo

2002-09-01

45

DArT markers for the rye genome - genetic diversity and mapping  

PubMed Central

Background Implementation of molecular breeding in rye (Secale cereale L.) improvement programs depends on the availability of high-density molecular linkage maps. However, the number of sequence-specific PCR-based markers available for the species is limited. Diversity Arrays Technology (DArT) is a microarray-based method allowing for detection of DNA polymorphism at several thousand loci in a single assay without relying on DNA sequence information. The objective of this study was the development and application of Diversity Arrays technology for rye. Results Using the PstI/TaqI method of complexity reduction we created a rye diversity panel from DNA of 16 rye varieties and 15 rye inbred lines, including parents of a mapping population consisting of 82 recombinant inbred lines. The usefulness of a wheat diversity panel for identification of DArT markers for rye was also demonstrated. We identified 1022 clones that were polymorphic in the genotyped ILs and varieties and 1965 clones that differentiated the parental lines L318 and L9 and segregated in the mapping population. Hierarchical clustering and ordination analysis were performed based on the 1022 DArT markers to reveal genetic relationships between the rye varieties and inbred lines included in the study. Chromosomal location of 1872 DArT markers was determined using wheat-rye addition lines and 1818 DArT markers (among them 1181 unique, non-cosegregating) were placed on a genetic linkage map of the cross L318 × L9, providing an average density of one unique marker every 2.68 cM. This is the most saturated rye linkage map based solely on transferable markers available at the moment, providing rye breeders and researches with a better choice of markers and a higher probability of finding polymorphic markers in the region of interest. Conclusion The Diversity Arrays Technology can be efficiently and effectively used for rye genome analyses - assessment of genetic similarity and linkage mapping. The 11520-clone rye genotyping panel with several thousand markers with determined chromosomal location and accessible through an inexpensive genotyping service is a valuable resource for studies on rye genome organization and in molecular breeding of the species.

2009-01-01

46

Genetic markers of an aboriginal Taiwanese population.  

PubMed

A group of Taiwan aborigines, the Toroko, was typed for 21 classical genetic loci. This is part of an ongoing program aimed at a comprehensive study of Taiwan aborigines. In this first paper a short summary of historical, archeological, and anthropological data in the literature is made, and results of the present survey are compared with older results from other aborigine tribes. An analysis of other neighboring populations from southeast Asia has also been carried out in order to give a preliminary answer to the question of origin of Taiwanese aborigines. Fifteen populations were studied for 13 loci by tree analysis, principal components, and isolation by distance. Tree analysis and principal component analysis gave results in fairly good agreement and indicate three major population clusters: a northeast cluster (Ainu, Korea, Japan, and Ryukyu); a southeast cluster (south China, Thailand, Vietnam, Philippines, Taiwan, and Toroko); and a third cluster including Malaya and Borneo. The positions of Polynesia, Micronesia, and Melanesia are somewhat peripheral. Analysis of the tree shows some potential cases of convergence, perhaps owing to admixture, and of divergence. The analysis of isolation by distance shows that geographic propinquity is a reasonably good predictor of general similarity in this area. PMID:3857010

Chen, K H; Cann, H; Chen, T C; Van West, B; Cavalli-Sforza, L

1985-03-01

47

Genetic markers and the coregonid problem  

USGS Publications Warehouse

Coregonid fishes are the forage base in many ecosystems in the northern hemisphere and they have traditionally been part of commercial and native fisheries. Coregonids display extreme variability in morphology, life history, and behavior. Defining boundaries among coregonid taxa has been (and continues to be) the focus of many studies. Cytogenetic, biochemical, and molecular methods have been used to study the 'coregonid problem'. A survey of the literature reveals that questions of taxonomy, followed by phylogeography are most often studied. Sample collections have occurred throughout a representative portion of the coregonid range. The whitefish species Coregonus clupeaformis and C. lavaretus are most often studied. This was expected however because they are the most widely distributed, display the most variation, and are the most commercially important. However, species with restricted ranges such as the Irish pollan (C. pollan) or omul (C. migratorius) have also been studied intensively. Genetic methods have provided insights into several issues, including the placement of Stenodus and the status of C. clupeaformis and C. lavaretus. More recently, studies of sympatric forms over broad geographic scales shed light on processes involved in the evolution of the group and suggest different approaches for management and designation of taxa. ?? 2007 E. Schweizerbart'sche Verlagsbuchhandlung.

Stott, W.; Todd, T. N.

2007-01-01

48

Drosophila hematopoiesis: Markers and methods for molecular genetic analysis.  

PubMed

Analyses of the Drosophila hematopoietic system are becoming more and more prevalent as developmental and functional parallels with vertebrate blood cells become more evident. Investigative work on the fly blood system has, out of necessity, led to the identification of new molecular markers for blood cell types and lineages and to the refinement of useful molecular genetic tools and analytical methods. This review briefly describes the Drosophila hematopoietic system at different developmental stages, summarizes the major useful cell markers and tools for each stage, and provides basic protocols for practical analysis of circulating blood cells and of the lymph gland, the larval hematopoietic organ. PMID:24613936

Evans, Cory J; Liu, Ting; Banerjee, Utpal

2014-06-15

49

Neural Markers of Genetic Vulnerability to Drug Addiction  

Microsoft Academic Search

\\u000a This chapter will summarize genetics findings derived from various strategies and highlight important neural markers (or correlates)\\u000a in some specific and extensively studied genes. Most studies highlighted here focus on alcohol and nicotine dependence (AD\\u000a and ND, respectively). AD and ND are among the most prevalent addictive disorders worldwide, are among the best studied, and\\u000a are also associated globally with

Daniel J. Müller; Olga Likhodi; Andreas Heinz

50

Assessment of genetic diversity in Azadirachta indica using AFLP markers  

Microsoft Academic Search

Genetic diversity was estimated in 37 neem accessions from different eco-geographic regions of India and four exotic lines\\u000a from Thailand using AFLP markers. Seven AFLP selective primer combinations generated a total of 422 amplification products.\\u000a The average number of scorable fragments was 60 per experiment, and a high degree (69.8%) of polymorphism was obtained per\\u000a assay with values ranging from

A. Singh; M. S. Negi; J. Rajagopal; S. Bhatia; U. K. Tomar; P. S. Srivastava; M. Lakshmikumaran

1999-01-01

51

Major histocompatibility locus genetic markers of beryllium sensitization and disease  

Microsoft Academic Search

Major histocompatibility locus genetic markers of beryllium sensitization and disease. C. Saltini, L. Richeldi, M. Losi, M. Amicosante, C. Voorter, E. van den Berg-Loonen, R.A. Dweik, H.P. Wiedemann, D.C. Deubner, C. Tinelli. #ERS Journals Ltd 2001. ABSTRACT: Hypersensitivity to beryllium (Be) is found in 1-16% of exposed workers undergoing immunological screening for beryllium disease using the beryllium lym- phocyte proliferation

C. Saltini; L. Richeldi; M. Losi; M. Amicosante; C. Voorter; E. Van Den Berg-Loonen; R. A. Dweik; H. P. Wiedemann; D. C. Deubner; C. Tinelli

2001-01-01

52

Genetic Kinship Investigation from Blood Groups to DNA Markers  

PubMed Central

The forensic application of hereditary characteristics became possible after the discovery of human blood groups by Karl Landsteiner in 1901. The foundation for their use in kinship investigation was laid by Emil von Dungern and Ludwig Hirschfeld in 1910 by clarification of the inheritance of the ABO groups. Up to the middle of the 20th century further red cell membrane systems were discovered. From the 1920s Fritz Schiff and Georg Strassmann fought for the introduction of blood groups into forensic kinship investigation. A new era of hemogenetics was opened from 1955 as genetic polymorphisms were described in serum proteins. Starting in 1958 there followed the complex HLA system of white blood cells, which from 1963 was joined by polymophisms in erythrocyte enzymes. Therefore, from the 1980s, it was possible to clarify the majority of kinship cases with a combination of conventional markers. From 1990 to 2000 the conventional markers were gradually replaced by the more effective DNA markers. Simultaneously typing shifted from the phenotype level to the genotype level. The genomic structure of conventional genetic markers could also now be explained. As a reflection of scientific progress the legal situation also changed, particularly in the form of the official guidelines for kinship investigation.

Geserick, Gunther; Wirth, Ingo

2012-01-01

53

Development and application of SINE multilocus and quantitative genetic markers to study oilseed rape (Brassica napus L.) crops.  

PubMed

A genetic marker system based on the S1 Short Interspersed Elements (SINEs) in the important commercial crop, oilseed rape ( Brassica napus L.) has been developed. SINEs provided a successful multilocus, dominant marker system that was capable of clearly delineating winter- and spring-type crop varieties. Sixteen of 20 varieties tested showed unique profiles from the 17 polymorphic SINE markers generated. The 3' or 5' flank region of nine SINE markers were cloned, and DNA was sequenced. In addition, one putative pre-transposition SINE allele was cloned and sequenced. Two SINE flanking sequences were used to design real-time PCR assays. These quantitative SINE assays were applied to study the genetic structure of eight fields of oilseed rape crops. Studied fields were more genetically diverse than expected for the chosen loci (mean H T = 0.23). The spatial distribution of SINE marker frequencies was highly structured in some fields, suggesting locations of volunteer impurities within the crop. In one case, the assay identified a mislabeling of the crop variety. SINE markers were a useful tool for crop genetics, phylogenetics, variety identification, and purity analysis. The use and further application of quantitative, real-time PCR markers are discussed. PMID:18092752

Allnutt, T R; Roper, K; Henry, C

2008-01-23

54

Genetic variability in Brazilian wheat cultivars assessed by microsatellite markers  

PubMed Central

Wheat (Triticum aestivum) is one of the most important food staples in the south of Brazil. Understanding genetic variability among the assortment of Brazilian wheat is important for breeding. The aim of this work was to molecularly characterize the thirty-six wheat cultivars recommended for various regions of Brazil, and to assess mutual genetic distances, through the use of microsatellite markers. Twenty three polymorphic microsatellite markers (PMM) delineated all 36 of the samples, revealing a total of 74 simple sequence repeat (SSR) alleles, i.e. an average of 3.2 alleles per locus. Polymorphic information content (PIC value) calculated to assess the informativeness of each marker ranged from 0.20 to 0.79, with a mean of 0.49. Genetic distances among the 36 cultivars ranged from 0.10 (between cultivars Ocepar 18 and BRS 207) to 0.88 (between cultivars CD 101 and Fudancep 46), the mean distance being 0.48. Twelve groups were obtained by using the unweighted pair-group method with arithmetic means analysis (UPGMA), and thirteen through the Tocher method. Both methods produced similar clusters, with one to thirteen cultivars per group. The results indicate that these tools may be used to protect intellectual property and for breeding and selection programs.

2009-01-01

55

Pedigree and marker information requirements to monitor genetic variability.  

PubMed

There are several measures available to describe the genetic variability of populations. The average inbreeding coefficient of a population based on pedigree information is a frequently chosen option. Due to the developments in molecular genetics it is also possible to calculate inbreeding coefficients based on genetic marker information. A simulation study was carried out involving ten sires and 50 dams. The animals were mated over a period of 20 discrete generations. The population size was kept constant. Different situations with regard to the level of polymorphism and initial allele frequencies and mating scheme (random mating, avoidance of full sib mating, avoidance of full sib and half sib mating) were considered. Pedigree inbreeding coefficients of the last generation using full pedigree or 10, 5 and 2 generations of the pedigree were calculated. Marker inbreeding coefficients based on different sets of microsatellite loci were also investigated. Under random mating, pedigree-inbreeding coefficients are clearly more closely related to true autozygosity (i.e., the actual proportion of loci with alleles identical by descent) than marker-inbreeding coefficients. If mating is not random, the demands on the quality and quantity of pedigree records increase. Greater attention must be paid to the correct parentage of the animals. PMID:12927072

Baumung, Roswitha; Sölkner, Johann

2003-01-01

56

[Distribution of genetic markers in offsprings of irradiated individuals].  

PubMed

For the estimation of radiation exposure on genetic processes in Mayak PA population we studied the distribution of a number of genetic markers in offsprings of Mayak PA workers depending on radiation (preconceptive and antenatal chronic exteral gamma-radiation) and non-radiation (age-sex characteristics of children and age characteristics of parents to the moment of conception) factors. Relatively unfavorable changes in distribution of genotypes and genes of haptoglobin genetic system in offsprings, whose parents (one or both) were exposed to external gamma-radiation in preconceptive cumulative dose of more than 200 cGy were detected. The most obvious reason of such changes may consist in directed gametic selection (Hp2 allele versus Hp1 allele) which turns out in abnormalities of segregation of Hp2-1 heterozygote that have both alleles. Effect of antenatal exposure on distribution of studied genetic markers in offspring of exposed population in studied dose range were not found. Homotypic changes in distribution of ABO bood groups and alleles in offspring of exposed and unexposed individuals depending on age characteristics of parents (middle age and age differences of both parents) for the moment of conception were also detected. PMID:19004327

Tel'nov, V I

2008-01-01

57

Population genetic structure of Central African Trypanosoma brucei gambiense isolates using microsatellite DNA markers  

Microsoft Academic Search

Genetic variation of microsatellite loci is a widely used method for the analysis of population genetic structure of microorganisms. Seven microsatellite markers were used here to characterize Trypanosoma brucei gambiense isolates from Central Africa sub-region in order to improve knowledge on the population genetic structure of this subspecies. These markers confirmed the low genetic polymorphism within Central African T. b.

Gustave Simo; Flobert Njiokou; Christopher Tume; Smiths Lueong; Thierry De Meeûs; Gerard Cuny; Tazoacha Asonganyi

2010-01-01

58

Genetic Markers Used for Risk Stratification in Multiple Myeloma  

PubMed Central

While no specific genetic markers are required in the diagnosis of multiple myeloma (MM), multiple genetic abnormalities and gene signatures are used in disease prognostication and risk stratification. This is particularly important for the adequate identification of the high-risk MM group, which does not benefit from any of the current therapies, and novel approaches need to be proposed. Fluorescence in situ hybridization (FISH) has been employed for establishing risk-based stratification and still remains the most used genetic technique in the clinical routine. The incorporation of gene expression profiling (GEP) in the study of MM has shown to be a very powerful test in the patient stratification, but its incorporation in clinical routine depends on some technical and logistic resolutions. Thus, FISH still remains the gold standard test for detecting genomic abnormalities and outcome discrimination in MM.

Segges, Priscilla; Braggio, Esteban

2011-01-01

59

Genetic characterization of fig tree mutants with molecular markers.  

PubMed

The fig (Ficus carica L.) is a fruit tree of great world importance and, therefore, the genetic improvement becomes an important field of research for better crops, being necessary to gather information on this species, mainly regarding its genetic variability so that appropriate propagation projects and management are made. The improvement programs of fig trees using conventional procedures in order to obtain new cultivars are rare in many countries, such as Brazil, especially due to the little genetic variability and to the difficulties in obtaining plants from gamete fusion once the wasp Blastophaga psenes, responsible for the natural pollinating, is not found in Brazil. In this way, the mutagenic genetic improvement becomes a solution of it. For this reason, in an experiment conducted earlier, fig plants formed by cuttings treated with gamma ray were selected based on their agronomic characteristics of interest. We determined the genetic variability in these fig tree selections, using RAPD and AFLP molecular markers, comparing them to each other and to the Roxo-de-Valinhos, used as the standard. For the reactions of DNA amplification, 140 RAPD primers and 12 primer combinations for AFLP analysis were used. The selections did not differ genetically between themselves and between them and the Roxo-de-Valinhos cultivar. Techniques that can detect polymorphism between treatments, such as DNA sequencing, must be tested. The phenotypic variation of plants may be due to epigenetic variation, necessitating the use of techniques with methylation-sensitive restriction enzymes. PMID:22911583

Rodrigues, M G F; Martins, A B G; Desidério, J A; Bertoni, B W; Alves, M C

2012-01-01

60

Genetic diversity analysis of common beans based on molecular markers  

PubMed Central

A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

Gill-Langarica, Homar R.; Muruaga-Martinez, Jose S.; Vargas-Vazquez, M.L. Patricia; Rosales-Serna, Rigoberto; Mayek-Perez, Netzahualcoyotl

2011-01-01

61

A unique case of female pseudohermaphroditism with 21-hydroxylase deficiency and small supernumerary marker chromosome 7.  

PubMed

Small supernumerary marker chromosomes (sSMCs) are present in ~2.6x10? individuals worldwide. Concerning their clinical consequences as well as their chromosomal origin and shape, sSMCs are a heterogeneous group of derivative chromosomes; 70% of sSMC carriers are clinically normal. In the present study, we report on a female with mosaicism (45%) of a de novo sSMC derived from chromosome 7, in which the observed clinical signs do not correspond to comparable cases in the literature. She is clinically normal apart from problems in gender determination, a uterus without ovaries and an external penis, pointing overall towards an adrenogenital syndrome (AGS). 21-Hydroxylase deficiency (21-OHD) is the most common cause of AGS. A corresponding analysis for underlying mutations in the CYP21A2 gene revealed a homozygous mutation c.518T>A (p.Ile173Asn) inherited from both non-related parents. Overall, in this study, we report a unique case of female pseudohermaphroditism, classified as a simple virilization form of 21-OHD having an additional minute-shaped chromosome 7 [min(7)(:p11.1->q11.23:)]. Notably, AGS was due to a mutation in the CYP21A2 gene located on chromosome 6. This is a further example that detection of an sSMC does not always resolve the clinical case. PMID:23450434

Al-Achkar, Walid; Wafa, Abdulsamad; Assaad, Manar; Ehlers, Christian; Liehr, Thomas

2013-05-01

62

An evaluation of sequence tagged microsatellite site markers for genetic analysis within Citrus and related species.  

PubMed

Microsatellites, also called sequence tagged microsatellite sites (STMSs), have become important markers for genome analysis but are currently little studied in plants. To assess the value of STMSs for analysis within the Citrus plant species, two example STMSs were isolated from an intergeneric cross between rangpur lime (Citrus x limonia Osbeck) and trifoliate orange (Poncirus trifoliata (L.) Raf.). Unique flanking primers were constructed for polymerase chain reaction amplification both within the test cross and across a broad range of citrus and related species. Both loci showed length variation between test cross parents with alleles segregating in a Mendelian fashion to progeny. Amplification across species showed the STMS flanking primers to be conserved in every genome tested. The traits of polymorphism, inheritance, and conservation across species mean that STMS markers are ideal for genome mapping within Citrus, which contains high levels of genetic variability. PMID:7774802

Kijas, J M; Fowler, J C; Thomas, M R

1995-04-01

63

Comparison of RAPD and RFLP genetic markers in determining genetic similarity among Brassica oleracea L. genotypes  

Microsoft Academic Search

Genetic similarity among 45 Brassica Oleracea genotypes was compared using two molecular markers, random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphisms (RFLPs). The genotypes included 37 broccolis (var. italica), five cauliflowers (var. botrytis) and three cabbages (var. capitata) which represented a wide range of commercially-available germplasm, and included open-pollinated cultivars, commercial hybrids, and inbred parents of hybrid cultivars.

J. B. dos Santos; J. Nienhuis; P. Skroch; J. Tivang; M. K. Slocum

1994-01-01

64

Development of the arbitrarily primed-representational difference analysis method and chromosomal mapping of isolated high throughput rat genetic markers  

PubMed Central

Linkage mapping of quantitative trait loci requires analysis of a large number of animals. Although genetic markers isolated by representational difference analysis (RDA) and its modifications meet the needs, the number of these markers has been limited. In the present study, we established the arbitrarily primed (AP)–RDA method to isolate virtually an unlimited number of the high throughput genetic markers. A representation of the genome, an AP-amplicon, was prepared by AP-PCR with a single primer or with a combination of primers using genomic DNA of the ACI/N (ACI) or BUF/Nac (BUF) rat as a template. By subtracting the AP-amplicon of ACI from that of BUF, a total of 40 polymorphic and independent markers were isolated in seven series of AP-RDA using a single primer. Two series of AP-RDA with primer combination yielded seven additional independent markers. All of the markers gave clear positive/negative signals by hybridization of a filter where AP-amplicons from F2 rats of ACI and BUF were dot-blotted at a high density without any concentration or purification. All of the 47 independent markers were mapped to unique chromosomal positions by linkage analysis, even though some arbitrary primers had very similar sequences. The markers were also informative between other strains of rats. Simultaneous hybridization of multiple filters made it possible to genotype a large number of rats simultaneously for multiple genetic loci. The AP-RDA method promises isolation of a large number of high throughput genetic markers in any species and is expected to facilitate linkage mapping of subtle quantitative trait loci.

Yoshida, Yukinari; Ushijima, Toshikazu; Yamashita, Satoshi; Imai, Kohzoh; Sugimura, Takashi; Nagao, Minako

1999-01-01

65

Genetic diversity in Hemileia vastatrix based on RAPD markers.  

PubMed

Random amplified polymorphic DNA (RAPD) was used to assess the genetic structure of Hemileia vastatrix populations. Forty-five rust isolates with different virulence spectra and from different hosts and geographical regions were analyzed. Out of 45 bands, generated with three RAPD primers, 35 (78%) were polymorphic and scored as molecular markers. Cluster analysis exhibits unstructured variability of this pathogen with regard to physiological race, geographical origin or host. The genotypic diversity (H') inferred from Shannon's index was higher than gene diversity (Ht), suggesting that diversity is distributed among clonal lineages. Estimates of gene diversity in Africa and Asia populations were higher in total (Ht) as compared to within population diversity (Hs). Genetic differentiation was considerable among coffee rust isolates from Africa (Gst = 0.865) and Asia (Gst = 0.768) but not among isolates from South America (Gst = 0.266). We concluded that genetic diversity in H. vastatrix was moderately low and that the genetic differentiation among populations shows that asexual reproduction is likely to play an important role in the population biology of this fungus. This should be taken into account for the development of breeding programs. PMID:16396347

Gouveia, M Manuela C; Ribeiro, Ana; Várzea, Vítor M P; Rodrigues, Carlos J

2005-01-01

66

Quantitative PCR for Genetic Markers of Human Fecal Pollution?  

PubMed Central

Assessment of health risk and fecal bacterial loads associated with human fecal pollution requires reliable host-specific analytical methods and a rapid quantification approach. We report the development of quantitative PCR assays for quantification of two recently described human-specific genetic markers targeting Bacteroidales-like cell surface-associated genes. Each assay exhibited a range of quantification from 10 to 1 × 106 copies of target DNA. For each assay, internal amplification controls were developed to detect the presence or absence of amplification inhibitors. The assays predominantly detected human fecal specimens and exhibited specificity levels greater than 97% when tested against 265 fecal DNA extracts from 22 different animal species. The abundance of each human-specific genetic marker in primary effluent wastewater samples collected from 20 geographically distinct locations was measured and compared to quantities estimated by real-time PCR assays specific for rRNA gene sequences from total Bacteroidales and enterococcal fecal microorganisms. Assay performances combined with the prevalence of DNA targets in sewage samples provide experimental evidence supporting the potential application of these quantitative methods for monitoring fecal pollution in ambient environmental waters.

Shanks, Orin C.; Kelty, Catherine A.; Sivaganesan, Mano; Varma, Manju; Haugland, Richard A.

2009-01-01

67

Automation of genetic linkage analysis using florescent microsatellite markers  

SciTech Connect

Automation of the typing of genetic markers offers advantages of speed, accuracy, and cost in the mapping of genetic traits and the construction of high-resolution linkage maps. The authors have developed an automated linkage analysis system by (i) using a robotic pipettor to set up polymerase chain reactions (PCR) to amplify microsatellites with incorporation of a single fluorescent label; (ii) using an automated sequencing apparatus for detection of the PCR products; (iii) sizing alleles automatically by the use of internal and external standards; (iv) iteratively filtering out nonallelic fragments and checking for Mendelian consistency; (v) calculating the probabilities of selected genotypes; and (vi) automatically formatting the results for input to linkage analysis programs. The method provides accurate sizing of alleles, minimizes the risk of error during manual reading and transcription of data, and increases the throughput of reliable data. It brings any consistencies or ambiguities in the data to the attention of the user and facilitates examination of the raw data. The ALF/ALP system, together with new, optimized microsatellite sets, particularly tetranucleotide repeats, is likely to be well-suited to fully automatic genetic linkage analysis. 32 refs., 2 figs., 2 tabs.

Mansfield, D.C.; Brown, A.F.; Green, D.K. [Western General Hospital, Edinburgh (United Kingdom)] [and others] [Western General Hospital, Edinburgh (United Kingdom); and others

1994-11-15

68

Genetic characterization of Barbari goats using microsatellite markers  

PubMed Central

Genetic variation in Barbari goats, a highly prolific breed distributed widely in the northern part of India, known for better milk and meat quality, was studied as a part of genetic characterization and conservation. The genomic DNA from 50 unrelated Barbari goats were amplified via PCR with a panel of 21 microsatellite markers, and resolved through 6 per cent denaturing polyacrylamide gel electrophoresis followed by silver staining. The number of alleles ranged from 4 to 11, with allele sizes ranging from 88 to 220 bp. The distribution of allele frequencies was between 0.0104 and 0.5208. Polymorphism information content varied from 0.5563 to 0.8348. The population was not in Hardy-Weinberg equilibrium for all except two microsatellite loci (ILSTS044 and ILSTS060). The observed heterozygosity ranged from 0.8478 to 1.0000 while the expected heterozygosity ranged from 0.6208 to 0.8509. Based on the results of the present study, there is a good scope for exploiting the genetic variability in the Barbari goats for further improvement of performance.

Ramamoorthi, J.; Thilagam, K.; Karthickeyan, S. M. K.

2009-01-01

69

Genetic diversity assessment of summer squash landraces using molecular markers.  

PubMed

Plant identification, classification, and genotyping within a germplasm collection are essential elements for establishing a breeding program that enhances the probability of plants with desirable characteristics in the market place. In this study, random amplified polymorphic DNA (RAPD) was used as a molecular tool to assess the diversity and relationship among 20 summer squash (Curcubita pepo L.) landraces traditionally used to treat hypertension and prostate hyperplasia. A total of 10 RAPD primers produced 65 reproducible bands of which 46 (70.77 %) were polymorphic, indicating a large number of genotypes within the summer squash lines. Cluster analysis divided the summer squash germplasm into two groups, one including one landrace and a second containing 19 landraces that could be divided into five sub-groups. Results of this study indicate the potential of RAPD markers for the identification and assessment of genetic variations among squash landraces and provide a number of choices for developing a successful breeding program to improve summer squash. PMID:23666102

Mady, Emad A; Helaly, Alaa Al-Din; Abu El-Hamd, Abdel Naem; Abdou, Arafa; Shanan, Shamel A; Craker, Lyle E

2013-07-01

70

How many marker loci are necessary? Analysis of dominant marker data sets using two popular population genetic algorithms  

PubMed Central

The number of marker loci required to answer a given research question satisfactorily is especially important for dominant markers since they have a lower information content than co-dominant marker systems. In this study, we used simulated dominant marker data sets to determine the number of dominant marker loci needed to obtain satisfactory results from two popular population genetic analyses: STRUCTURE and AMOVA (analysis of molecular variance). Factors such as migration, level of population differentiation, and unequal sampling were varied in the data sets to mirror a range of realistic research scenarios. AMOVA performed well under all scenarios with a modest quantity of markers while STRUCTURE required a greater number, especially when populations were closely related. The popular ?K method of determining the number of genetically distinct groups worked well when sampling was balanced, but underestimated the true number of groups with unbalanced sampling. These results provide a window through which to interpret previous work with dominant markers and we provide a protocol for determining the number of markers needed for future dominant marker studies.

Nelson, Michael F; Anderson, Neil O

2013-01-01

71

Genetic markers for diagnosis and pathogenesis of Alzheimer's disease.  

PubMed

Alzheimer's disease (AD) is the most common form of dementia in the elderly and represents an important and increasing clinical challenge in terms of diagnosis and treatment. Mutations in the genes encoding amyloid precursor protein (APP), presenilin 1 (PSEN1) and presenilin 2 (PSEN2) are responsible for early-onset autosomal dominant AD. The ?4 allele of the apolipoprotein E (APOE) gene has been recognized as a major genetic risk factor for the more common, complex, late-onset AD. Fibrillar deposits by phosphorylated tau are also a key pathological feature of AD. The retromer complex also has been reported to late-onset AD. More recently, genome-wide association studies (GWASs) identified putative novel candidate genes associated with late-onset AD. Lastly, several studies showed that circulating microRNAs (miRNAs) in the cerebrospinal fluid (CSF) and blood serum of AD patients can be used as biomarkers in AD diagnosis. This review addresses the advances and challenges in determining genetic and diagnostic markers for complex AD pathogenesis. PMID:24838203

Kim, Dong Hee; Yeo, Seung Hyeon; Park, Jeong-Min; Choi, Ji Ye; Lee, Tae-Hee; Park, Soon Yong; Ock, Mee Sun; Eo, Jungwoo; Kim, Heui-Soo; Cha, Hee-Jae

2014-07-25

72

Genome-wide genetic marker discovery and genotyping using next-generation sequencing  

Microsoft Academic Search

The advent of next-generation sequencing (NGS) has revolutionized genomic and transcriptomic approaches to biology. These new sequencing tools are also valuable for the discovery, validation and assessment of genetic markers in populations. Here we review and discuss best practices for several NGS methods for genome-wide genetic marker development and genotyping that use restriction enzyme digestion of target genomes to reduce

Paul A. Hohenlohe; Paul D. Etter; Jason Q. Boone; Julian M. Catchen; Mark L. Blaxter; John W. Davey

2011-01-01

73

A genetic linkage map of crested wheatgrass based on AFLP and RAPD markers.  

PubMed

Using a population of 105 interspecific F(2) hybrids derived from a cross between Agropyron mongolicum Keng and Agropyron cristatum (L.) Gaertn. 'Fairway' as a mapping population, a genetic linkage map of crested wheatgrass was constructed based on AFLP and RAPD molecular markers. A total of 175 markers, including 152 AFLP and 23 RAPD markers, were ordered in seven linkage groups. The map distance was 416 cM, with a mean distance of 2.47 cM between markers. The number of markers ranged from 13 to 46 in each linkage group and the length of groups ranged from 18 to 104 cM. The research found that 30 out of 175 molecular markers showed segregation distortion, accounting for 17% of all markers. This is the first genetic linkage map of crested wheatgrass. This map will facilitate gene localization, cloning, and molecular marker-assisted selection in the future. PMID:22462407

Yu, Xiaoxia; Li, Xiaolei; Ma, Yanhong; Yu, Zhuo; Li, Zaozhe

2012-03-30

74

Associations of genetic markers in cattle receiving differing implant protocols.  

PubMed

The potential interaction of growth-promoting implants and genetic markers previously reported to be associated with growth, carcass traits, and tenderness was evaluated. Two implant protocols were applied to subsets of steers (n = 383) and heifers (n = 65) that were also genotyped for 47 SNP reported to be associated with variation in growth, fat thickness, LM area, marbling, or tenderness. The "mild" protocol consisted of a single terminal implant [16 mg estradiol benzoate (EB), 80 mg trenbalone acetate (TBA) or 8 mg EB, 80 mg TBA given to steers and heifers, respectively]. The "aggressive" protocol consisted of both a growing implant (8 mg EB, 40 mg TBA) for the lightest half of the animals on the aggressive protocol and 2 successive implants (28 mg EB, 200 mg TBA) given to all animals assigned to the aggressive treatment. Implant protocol had measurable impact on BW and ADG (P < 0.05), with the aggressive protocol increasing these traits before the terminal implant (relative to the mild protocol), whereas the mild protocol increased ADG after the terminal implant so that the final BW and ADG over the experimental period were similar between protocols. Animals on the aggressive protocol had significantly increased (P < 0.05) LM area (1.9 cm(2)), slice shear force (1.4 kg), and intact desmin (0.05 units), but decreased (P < 0.05) marbling score (49 units) and adjusted fat thickness (0.1 cm), and yield grade (0.15 units). Among both treatments, 8 of 9 growth-related SNP were associated with BW or ADG, and 6 of 17 tenderness-related SNP were associated with slice shear force or intact desmin. Favorable growth alleles generally were associated with increased carcass yield traits but decreased tenderness. Similarly, favorable tenderness genotypes for some markers were associated with decreased BW and ADG. Some interactions of implant protocol and genotype were noted, with some growth SNP alleles increasing the effect of the aggressive protocol. In contrast, putative beneficial effects of favorable tenderness SNP alleles were mitigated by the effects of aggressive implant. These type of antagonisms of management variables and genotypes must be accounted for in marker assisted selection (MAS) programs, and our results suggest that MAS could be used to manage, but likely will not eliminate negative impact of implants on quality. PMID:22767554

King, D A; Shackelford, S D; McDaneld, T G; Kuehn, L A; Kemp, C M; Smith, T P L; Wheeler, T L; Koohmaraie, M

2012-07-01

75

Psychological aspects of human cloning and genetic manipulation: the identity and uniqueness of human beings.  

PubMed

Human cloning has become one of the most controversial debates about reproduction in Western civilization. Human cloning represents asexual reproduction, but the critics of human cloning argue that the result of cloning is not a new individual who is genetically unique. There is also awareness in the scientific community, including the medical community, that human cloning and the creation of clones are inevitable. Psychology and other social sciences, together with the natural sciences, will need to find ways to help the healthcare system, to be prepared to face the new challenges introduced by the techniques of human cloning. One of those challenges is to help the healthcare system to find specific standards of behaviour that could be used to help potential parents to interact properly with cloned babies or children created through genetic manipulation. In this paper, the concepts of personality, identity and uniqueness are discussed in relationship to the contribution of twin studies in these areas. The author argues that an individual created by human cloning techniques or any other type of genetic manipulation will not show the donor's characteristics to the extent of compromising uniqueness. Therefore, claims to such an effect are needlessly alarmist. PMID:19891847

Morales, N M

2009-01-01

76

[Progress in InDel as a new generation of genetic marker].  

PubMed

As forensic DNA typing experienced three generations of genetic marker researching stage, short tandem repeat (STR) has been widely used in forensic identification as a mature tool. Further exploration of the human genome led to the discovery of polymorphism markers of single nucleotide polymorphism (SNP) and Insertion/Deletion (InDel). InDel, which combines the desirable characteristics of previous genetic markers as a new type of genetic marker, has got extensive concern in fields like medical molecular biology and forensic biology. This paper generally reviews the history of research and the corresponding results of InDel along the line of time axis as well as the different aims of these research focusing on the progress in the multiple amplification system with several InDel as the genetic marker (autosomal or X chromosome) in forensic biology and anthropology. Finally, the direction of research in this field and the problems to be solved have been put forward. PMID:23930511

Sun, Kuan; Zhang, Su-Hua; Zhu, Ru-Xin; Zhao, Shu-Min; Li, Cheng-Tao

2013-04-01

77

Alu repeats as markers for human population genetics  

SciTech Connect

The Human-Specific (HS) subfamily of Alu sequences is comprised of a group of 500 nearly identical members which are almost exclusively restricted to the human genome. Individual subfamily members share an average of 97.9% nucleotide identity with each other and an average of 98.9% nucleotide identity with the HS subfamily consensus sequence. HS Alu family members are thought to be derived from a single source ``master`` gene, and have an average age of 2.8 million years. We have developed a Polymerase Chain Reaction (PCR) based assay using primers complementary to the 5 in. and 3 in. unique flanking DNA sequences from each HS Alu that allows the locus to be assayed for the presence or absence of an Alu repeat. Individual HS Alu sequences were found to be either monomorphic or dimorphic for the presence or absence of each repeat. The monomorphic HS Alu family members inserted in the human genome after the human/great ape divergence (which is thought to have occurred 4--6 million years ago), but before the radiation of modem man. The dimorphic HS Alu sequences inserted in the human genome after the radiation of modem man (within the last 200,000-one million years) and represent a unique source of information for human population genetics and forensic DNA analyses. These sites can be developed into Dimorphic Alu Sequence Tagged Sites (DASTS) for the Human Genome Project as well. HS Alu family member insertion dimorphism differs from other types of polymorphism (e.g. Variable Number of Tandem Repeat [VNTR] or Restriction Fragment Length Polymorphism [RFLP]) because individuals share HS Alu family member insertions based upon identity by descent from a common ancestor as a result of a single event which occurred one time within the human population. The VNTR and RFLP polymorphisms may arise multiple times within a population and are identical by state only.

Batzer, M.A.; Alegria-Hartman, M. [Lawrence Livermore National Lab., CA (United States); Bazan, H. [Louisiana State Univ., New Orleans, LA (United States). Medical Center] [and others

1993-09-01

78

[Population genetic study of Russian cosmonauts and test subjects: genetic demographic parameters and immunogenetic markers].  

PubMed

Genetic demographic characteristics and immunogenetic markers (blood groups ABO, Rhesus, MNSs, P, Duffy, Kidd, and Kell) have been studied in a group of 132 Russian cosmonauts and test subjects (CTSG). Analysis of pedigrees has shown a high exogamy in the preceding generations: almost half of the subjects have mixed ethnic background. According to the results of genetic demographic analysis, a sample from the Moscow population was used as control group (CG). Comparison between the CTSG and CG has demonstrated significant differences in genotype frequencies for several blood group systems. The CTSG is characterized by a decreased proportion of rare interlocus genotypic combinations and an increased man heterozygosity. Analysis of the distributions of individual heterozygosity for loci with codominant expression of alleles has shown that highly heterozygous loci are more frequent in the CTSG. Taking into account that the CTSG has been thoroughly selected from the general population, it is concluded that heterozygosity is related to successful adaptation to a space flight. PMID:17152711

Kurbatova, O L; Pobedonostseva, E Iu; Prokhorovskaia, V D; Kholod, O N; Evsiukov, A N; Bogomolov, V V; Voronkov, Iu I; Filatova, L M; Larina, O N; Sidorenko, L A; Morgun, V V; Kasparanski?, R R; Altukhov, Iu P

2006-10-01

79

Autism and genetics: Clinical approach and association study with two markers of HRAS gene  

SciTech Connect

Twin studies and familial aggregation studies indicate that genetic factors could play a role in infantile autism. In an earlier study, we identified a possible positive association between autism and a c-Harvey-ras (HRAS) oncogene marker at the 3{prime} end of the coding region. In an attempt to confirm this finding, we studied a larger population, well-characterized clinically and genetically. We report a positive association between autism and two HRAS markers, the 3{prime} marker used in the initial study and an additional marker in exon 1. 46 refs., 1 fig., 2 tabs.

Herault, J.; Petit, E.; Cherpi, C. [Laboratoire de Biochimie Medicale, Tours (France)] [and others

1995-08-14

80

Impact of Marker Ascertainment Bias on Genomic Selection Accuracy and Estimates of Genetic Diversity  

PubMed Central

Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS) is rapidly emerging as a low-cost genotyping platform, even for the large, complex, and polyploid wheat (Triticum aestivum L.) genome. With GBS, marker discovery and genotyping occur simultaneously, resulting in minimal ascertainment bias. The previous platform of choice for whole-genome genotyping in many species such as wheat was DArT (Diversity Array Technology) and has formed the basis of most of our knowledge about cereals genetic diversity. This study compared GBS and DArT marker platforms for measuring genetic diversity and genomic selection (GS) accuracy in elite U.S. soft winter wheat. From a set of 365 breeding lines, 38,412 single nucleotide polymorphism GBS markers were discovered and genotyped. The GBS SNPs gave a higher GS accuracy than 1,544 DArT markers on the same lines, despite 43.9% missing data. Using a bootstrap approach, we observed significantly more clustering of markers and ascertainment bias with DArT relative to GBS. The minor allele frequency distribution of GBS markers had a deficit of rare variants compared to DArT markers. Despite the ascertainment bias of the DArT markers, GS accuracy for three traits out of four was not significantly different when an equal number of markers were used for each platform. This suggests that the gain in accuracy observed using GBS compared to DArT markers was mainly due to a large increase in the number of markers available for the analysis.

Heslot, Nicolas; Rutkoski, Jessica; Poland, Jesse; Jannink, Jean-Luc; Sorrells, Mark E.

2013-01-01

81

Genetic characterization of Blueberry necrotic ring blotch virus, a novel RNA virus with unique genetic features.  

PubMed

A new disorder was observed on southern highbush blueberries in several south-eastern states in the USA. Symptoms included irregularly shaped circular spots or blotches with green centres on the upper and lower surfaces of leaves. Double-stranded RNA was extracted from symptomatic leaves suggesting the presence of virus(es) possibly involved in the disease. Sequencing revealed the presence of a novel RNA virus with a ~14 kb genome divided into four RNA segments. Sequence analyses showed that the virus, for which we propose the name Blueberry necrotic ring blotch virus (BNRBV), possesses protein domains conserved across RNA viruses in the alpha-virus-like supergroup. Phylogenetic inferences using different genes placed BNRBV in a clade that includes the Bromoviridae, the genus Cilevirus (CiLV) and the recently characterized Hibiscus green spot virus (HGSV). Despite the strong genetic relationships found among BNRBV, Cilevirus and HGSV, the genome of BNRBV contains three features that distinguish it significantly from its closest relatives: (i) the presence of two helicase domains with different evolutionary pathways, (ii) the existence of three conserved nucleotide stretches located at the 3' non-coding regions of each RNA segment and (iii) the conservation of terminal nucleotide motifs across each segment. Furthermore, CiLV and HGSV possess poly(A)-tailed bipartite and tripartite genomes, respectively, whereas BNRBV has a quadra-partite genome lacking a poly(A) tail. Based on these genetic features a new genus is proposed for the classification of BNRBV. PMID:23486668

Quito-Avila, Diego F; Brannen, Philip M; Cline, William O; Harmon, Philip F; Martin, Robert R

2013-06-01

82

Erratum: Levels of genetic polymorphism: marker loci versus quantitative traits  

Microsoft Academic Search

Species are the units used to measure ecological diversity and alleles are the units of genetic diversity. Genetic variationwithin and among species hasbeen documented most extensively using allozyme electro- phoresis. This reveals wide di¡erences in genetic variability within, and genetic distances among, species, demonstrating that species are not equivalent units of diversity. The extent to which the pattern observed for

R. K. Butler; T. Tregenza

1998-01-01

83

Genetic assessment of safflower (Carthamus tinctorius L.) collection with microsatellite markers acquired via pyrosequencing method.  

PubMed

A genetic evaluation of safflower germplasm collections derived from different geographical regions and countries will provide useful information for sustainable conservation and the utilization of genetic diversity. However, the molecular marker information is limited for evaluation of genetic diversity of safflower germplasm. In this study, we acquired 509 putative genomic SSR markers for sufficient genome coverage using next-generation sequencing methods and characterized thirty polymorphic SSRs in safflower collection composed of 100 diverse accessions. The average allele number and expected heterozygosity were 2.8 and 0.386, respectively. Analysis of population structure and phylogeny based on thirty SSR profiles revealed genetic admixture between geographical regions contrary to genetic clustering. However, the accessions from Korea were genetically conserved in distinctive groups in contrast to other safflower gene pool. In conclusion, these new genomic SSRs will facilitate valuable studies to clarify genetic relationships as well as conduct population structure analyses, genetic map construction and association analysis for safflower. PMID:23875976

Lee, Gi-An; Sung, Jung-Sook; Lee, Sok-Young; Chung, Jong-Wook; Yi, Jung-Yoon; Kim, Yeon-Gyu; Lee, Myung-Chul

2014-01-01

84

Use of toxicogenomics for identifying genetic markers of pulmonary oedema  

SciTech Connect

This study was undertaken primarily to identify genetic markers of oedema and inflammation. Mild pulmonary injury was induced following the instillation of the oedema-producing agent, bleomycin (0.5 units). Oedema was then confirmed by conventional toxicology (lavage protein levels, free cell counts and lung/body weight ratios) and histology 3 days post-bleomycin instillation.The expression profile of 1176 mRNA species was determined for bleomycin-exposed lung (Clontech Atlas macroarray, n = 9). To obtain pertinent results from these data, it was necessary to develop a simple, effective method for bioinformatic analysis of altered gene expression. Data were log{sub 10} transformed followed by global normalisation. Differential gene expression was accepted if: (a) genes were statistically significant (P {<=} 0.05) from a two-tailed t test; (b) genes were consistently outside a two standard deviation (SD) range from control levels. A combination of these techniques identified 31 mRNA transcripts (approximately 3%) which were significantly altered in bleomycin treated tissue. Of these genes, 26 were down-regulated whilst only five were up-regulated. Two distinct clusters were identified, with 17 genes classified as encoding hormone receptors, and nine as encoding ion channels. Both these clusters were consistently down-regulated.The magnitude of the changes in gene expression were quantified and confirmed by Q-PCR (n = 6), validating the macroarray data and the bioinformatic analysis employed.In conclusion, this study has developed a suitable macroarray analysis procedure and provides the basis for a better understanding of the gene expression changes occurring during the early phase of drug-induced pulmonary oedema.

Balharry, Dominique [Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3US (United Kingdom)]. E-mail: balharry@cf.ac.uk; Oreffo, Victor [AstraZeneca, Loughborough, Leicestershire, LE11 5RH (United Kingdom); Richards, Roy [Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3US (United Kingdom)

2005-04-15

85

Isolation and Characterization of Microsatellite Markers and Analysis of Genetic Diversity in Chinese Jujube (Ziziphus jujuba Mill.)  

PubMed Central

Chinese jujube (Ziziphus jujuba Mill, 2n?=?2×?=?24, Rhamnaceae) is an economically important Chinese native species. It has high nutritional value, and its medicinal properties have led to extensive use in traditional oriental medicine. The characterization of genotypes using molecular markers is important for genetic studies and plant breeding. However, few simple sequence repeat (SSR) markers are available for this species. In this study, 1,488 unique SSR clones were isolated from Z. jujuba ‘Dongzao’ using enriched genomic libraries coupled with a three-primer colony PCR screening strategy, yielding a high enrichment rate of 73.3%. Finally, 1,188 (80.87%) primer pairs were amplified successfully in the size expected for ‘Dongzao’. A total of 350 primer pairs were further selected and evaluated for their ability to detect polymorphisms across a panel of six diverse cultivars; among these, 301 primer pairs detected polymorphisms, and the polymorphism information content (PIC) value across all loci ranged from 0.15 to 0.82, with an average of 0.52. An analysis of 76 major cultivars employed in Chinese jujube production using 31 primer pairs revealed comparatively high genetic diversity among these cultivars. Within-population differences among individuals accounted for 98.2% of the observed genetic variation. Neighbor-joining clustering divided the cultivars into three main groups, none of which correspond to major geographic regions, suggesting that the genetics and geographical origin of modern Chinese jujube cultivars might not be linked. The current work firstly reports the large-scale development of Chinese jujube SSR markers. The development of these markers and their polymorphic information represent a significant improvement in the available Chinese jujube genomic resources and will facilitate both genetic and breeding applications, further accelerating the development of new cultivars.

Liu, Huabo; Tang, Yan; Wu, Liping; Wang, Zhe; Li, Yingyue; Wu, Rongling; Pang, Xiaoming

2014-01-01

86

Isolation and Characterization of Microsatellite Markers and Analysis of Genetic Diversity in Chinese Jujube (Ziziphus jujuba Mill.).  

PubMed

Chinese jujube (Ziziphus jujuba Mill, 2n?=?2×?=?24, Rhamnaceae) is an economically important Chinese native species. It has high nutritional value, and its medicinal properties have led to extensive use in traditional oriental medicine. The characterization of genotypes using molecular markers is important for genetic studies and plant breeding. However, few simple sequence repeat (SSR) markers are available for this species. In this study, 1,488 unique SSR clones were isolated from Z. jujuba 'Dongzao' using enriched genomic libraries coupled with a three-primer colony PCR screening strategy, yielding a high enrichment rate of 73.3%. Finally, 1,188 (80.87%) primer pairs were amplified successfully in the size expected for 'Dongzao'. A total of 350 primer pairs were further selected and evaluated for their ability to detect polymorphisms across a panel of six diverse cultivars; among these, 301 primer pairs detected polymorphisms, and the polymorphism information content (PIC) value across all loci ranged from 0.15 to 0.82, with an average of 0.52. An analysis of 76 major cultivars employed in Chinese jujube production using 31 primer pairs revealed comparatively high genetic diversity among these cultivars. Within-population differences among individuals accounted for 98.2% of the observed genetic variation. Neighbor-joining clustering divided the cultivars into three main groups, none of which correspond to major geographic regions, suggesting that the genetics and geographical origin of modern Chinese jujube cultivars might not be linked. The current work firstly reports the large-scale development of Chinese jujube SSR markers. The development of these markers and their polymorphic information represent a significant improvement in the available Chinese jujube genomic resources and will facilitate both genetic and breeding applications, further accelerating the development of new cultivars. PMID:24932973

Wang, Siqi; Liu, Ying; Ma, Liying; Liu, Huabo; Tang, Yan; Wu, Liping; Wang, Zhe; Li, Yingyue; Wu, Rongling; Pang, Xiaoming

2014-01-01

87

Genetic markers for the identification and characterization of Opisthorchis viverrini, a medically important food borne trematode in Southeast Asia  

PubMed Central

The liver fluke, Opisthorchis viverrini, is one of the major food borne trematodes in Southeast Asia, where infection causes hepatobiliary disease and subsequent development of cholangiocarcinoma. In Thailand, O. viverrini is most prevalent in the northeast where there is marked regional variation in the rate of infection in humans at provincial, district and village levels. To date, the roles of genetic variation of O. viverrini on this observed variability in infection, transmission and associated disease are not known. We have applied multilocus enzyme electrophoresis (MEE), specifically allozyme electrophoresis, to isolates of O. viverrini from Thailand and Laos to establish genetic markers to examine its systematics and population structure. Forty-six enzymes commonly found useful for genetic characterisation in parasitic helminths were screened, and of these, 33 enzymes gave sufficient staining and resolution to act as potential genetic markers. Sixteen enzymes were monomorphic and 17 enzymes were polymorphic in the pools of worms examined. Whether they are indicative of different enzyme loci, heterozygosity or unique genotypes within the pools of worms examined remains to be determined. Preliminary investigations examining five individual worms at enzyme loci where pools of worms showed multiple bands have confirmed the diagnostic value of the enzyme loci established as well as providing evidence of potential population sub structuring and heterozygosity. For the first time, we have established at least 17 enzymes that provide the basis to undertake comprehensive genetic analyses of the systematics and population structure of O. viverrini, a medically important food borne trematode in Southeast Asia.

Saijuntha, Weerachai; Sithithaworn, Paiboon; Wongkham, Sopit; Laha, Thewarach; Pipitgool, Vichit; Petney, Trevor N; Andrews, Ross H

2006-01-01

88

[Genetic polymorphism of flax Linum usitatissimum based on use of molecular cytogenetic markers].  

PubMed

Using a set of approaches based on the use of molecular cytogenetic markers (DAPI/C-banding, estimation of the total area of DAPI-positive regions in prophase nuclei, FISH with 26S and 5S rDNA probes) and the microsatellite (SSR-PCR) assay, we studied genomic polymorphism in 15 flax (Linum usitatissimum L.) varieties from different geographic regions belonging to three directions of selection (oil, fiber, and intermediate flaxes) and in the k-37 x Viking hybrid. All individual chromosomes have been identified in the karyotypes of these varieties on the basis of the patterns of differential DAPI/C-banding and the distribution of 26S and 5S rDNA, and idiograms of the chromosomes have been generated. Unlike the oil flax varieties, the chromosomes in the karyotypes of the fiber flax varieties have, as a rule, pericentromeric and telomeric DAPI-positive bands of smaller size, but contain larger intercalary regions. Two chromosomal rearrangements (chromosome 3 inversions) were discovered in the variety Luna and in the k-37 x Viking hybrid. In both these forms, no colocalization of 26S rDNA and 5S rDNA on the satellite chromosome was detected. The SSR assay with the use of 20 polymorphic pairs of primers revealed 22 polymorphic loci. Based on the SSR data, we analyzed genetic similarity of the flax forms studied and constructed a genetic similarity dendrogram. The genotypes studied here form three clusters. The oil varieties comprise an independent cluster. The genetically related fiber flax varieties Vita and Luna, as well as the landrace Lipinska XIII belonging to the intermediate type, proved to be closer to the oil varieties than the remaining fiber flax varieties. The results of the molecular chromosomal analysis in the fiber and oil flaxes confirm their very close genetic similarity. In spite of this, the combined use of the chromosomal and molecular markers has opened up unique possibilities for describing the genotypes of flax varieties and creating their genetic passports. PMID:21446184

Rachinskaia, O A; Lemesh, V A; Muravenko, O V; Iurkevich, O Iu; Guzenko, E V; Bol'sheva, N L; Bogdanova, M V; Samatadze, T E; Popov, K V; Malyshev, S V; Shostak, N G; Heller, K; Khotyleva, L V; Zelenin, A V

2011-01-01

89

Genetic diversity in apricot cultivars based on AFLP markers  

Microsoft Academic Search

A set of cultivars used as genitors in apricot breeding programs aimed at introducing sharka resistance were examined by AFLP\\u000a molecular marker analysis. The markers obtained indicated that apricot cultivars resistant to sharka were related to the European\\u000a cultivars, but they potentially share a common ancestor donor of sharka outside of the European group. Segregation of AFLP\\u000a and RAPD markers

M. A. Hurtado; A. Westman; E. Beck; G. A. Abbott; G. Llácer; M. L. Badenes

2002-01-01

90

Population genetic study of Fagopyrum tataricum from Western Himalaya using ISSR markers.  

PubMed

Inter-simple sequence repeat (ISSR) markers were used to analyze genetic diversity and relatedness of 15 germplasms of Fagopyrum tataricum. Samples representing 75 individuals were collected from a range of altitudes in the Western Himalaya. The 13 ISSR primers revealed 98.1% polymorphism among populations, whereas average polymorphism was extremely low (2.18%) within populations. The coefficient of population differentiation was 0.9750, with limited gene flow (N m) of 0.0128. The average PIC value of the ISSR markers was high (0.812), with a marker ratio of 0.65 and marker index of 6.66. The genetic diversity of F. tataricum significantly correlated with altitude and gene diversity, Shannon's index, and the percentage of polymorphic bands. The genetic diversity among populations showed broad genetic base and provided a developmental strategy for crop improvement. PMID:23743875

Kishore, Garima; Pandey, Anjana; Dobhal, Rajendra; Gupta, Sanjay

2013-10-01

91

Functional genetic polymorphisms in cytokines and metabolic genes as additional genetic markers for susceptibility to develop type 1 diabetes  

Microsoft Academic Search

Genetic association with type 1 diabetes (T1D) has been established for two chromosomal regions: HLA DQ\\/DR (IDDM1) and INS VNTR (IDDM2). To identify additional genetic markers, we tested polymorphisms in regulatory regions of several cytokine and important metabolic genes. These polymorphisms exhibit functional consequences for expression and function. Functional genetic polymorphisms of proinflammatory (T-helper-1: IL-2, IL-12 and IFN-?), anti-inflammatory (T-helper-2:

P Eerligh; B P C Koeleman; F Dudbridge; G Jan Bruining; B O Roep; M J Giphart; BPC Koeleman

2004-01-01

92

Evolution of genetic and genomic features unique to the human lineage  

PubMed Central

Given the unprecedented tools now available for rapidly comparing genomes, the identification and study of genetic and genomic changes unique to our species has accelerated, and we are entering a golden age of human evolutionary genomics. Here we provide an overview of these efforts, highlighting important recent discoveries, examples of the different types of human-specific genomic and genetic changes identified, and salient trends such as the localization of evolutionary adaptive changes to complex loci that are highly enriched for disease associations. Lastly, we discuss the remaining challenges, such as the incomplete nature of current genome sequence assemblies, and difficulties in linking human-specific genomic changes to human-specific phenotypic traits.

O'Bleness, Majesta; Searles, Veronica; Varki, Ajit; Gagneux, Pascal; Sikela, James M.

2014-01-01

93

Genetically defined subsets of human pancreatic cancer demonstrate unique in vitro chemosensitivity  

PubMed Central

Purpose Pancreatic cancer (PC) is the fourth cause of death from cancer in the western world. Majority of patients present with advanced unresectable disease responding poorly to most chemotherapeutic agents. Chemotherapy for PC might be improved by adjusting it to individual genetic profiles. We attempt to identify genetic predictors of chemosensitivity to broad classes of anticancer drugs. Experimental Design Using a panel of genetically defined human PC cell lines, we tested gemcitabine (anti-metabolite), docetaxel (anti-microtubule), mitomycin C (alkylating), irinotecan (topoisomerase I inhibitor), cisplatin (crosslinking), KU0058948 (Parp1 inhibitor), triptolide (terpenoid drug) and artemisinin (control). Results All PC cell lines were sensitive to triptolide and docetaxel. Most PC cells were also sensitive to gemcitabine and MMC. The vast majority of PC cell lines were insensitive to cisplatin, irinotecan, and a Parp1 inhibitor. However, individual cell lines were often sensitive to these compounds in unique ways. We found that DPC4/SMAD4 inactivation sensitized PC cells to cisplatin and irinotecan by 2–4 fold, but they were modestly less sensitive to gemcitabine. PC cells were all sensitive to triptolide and 18% were sensitive to the Parp1 inhibitor. P16/CDKN2A inactivated PC cells were 3–4 fold less sensitive to gemcitabine and MMC. Conclusions Chemosensitivity of PC cells correlated with some specific genetic profiles. These results support the hypothesis that genetic subsets of pancreatic cancer exist, and these genetic backgrounds may permit one to personalize the chemotherapy of PC in the future. Further work will need to confirm these responses and determine their magnitude in vivo.

Cui, Yunfeng; Brosnan, Jacqueline A.; Blackford, Amanda; Sur, Surojit; Hruban, Ralph H.; Kinzler, Kenneth W.; Vogelstein, Bert; Maitra, Anirban; Diaz, Luis A.; Iacobuzio-Donahue, Christine A.; Eshleman, James R.

2012-01-01

94

Genetic analysis of the fragile-X mental retardation syndrome with two flanking polymorphic DNA markers  

SciTech Connect

The fragile-X mental retardation syndrome, one of the most prevalent chromosome X-linked diseases (approx. = 1 of 2000 newborn males), is characterized by the presence in affected males and in a portion of carrier females of a fragile site at chromosome band Xq27. The authors have performed a linkage analysis in 16 families between the locus for the fragile-X syndrome, FRAXQ27, and two polymorphic DNA markers that correspond to the anonymous probe St14 and to the coagulation factor IX gene F9. The results indicate that the order of loci is centromere-F9-FRAXQ27-St14-Xqter. The estimate of the recombination fraction for the linkage F9-FRAXQ27 is 0.12 and 0.10 for FRAXQ27-St14. Recombination between St14 and F9 does not appear to be significantly different in normal and fragile-X families. The two flanking probes were used for diagnosis of the carrier state and for detection of transmission of the disease through phenotypically normal males. They should also allow first-trimester diagnosis with a reliability of about 98% in 40% of the families. Used in conjunction with the cytogenetic analysis, the segregation studies with both probes should improve the genetic counseling for the fragile-X syndrome and should be useful for the formal genetic analysis of this unique disease.

Oberle, I.; Heilig, R.; Moisan, J.P.; Kloepfer, C.; Mattei, M.G.; Mattei, J.F.; Boue, J.; Froster-Iskenius, U.; Jacobs, P.A.; Lathrop, G.M.; Lalouel, J.M.

1986-02-01

95

The genetic structure of tetraploid Avena: a comparison of isozyme and RAPD markers.  

PubMed

Isozymes were the first widely used molecular markers in plant population analysis. They yielded valuable information on the amount and the structure of genetic variability. DNA technology has provided new types of markers based on DNA sequence, which make it possible to study polymorphisms in a much greater proportion of the genome. This is the reason why the use of isozymes is less popular nowadays. This effect would be justified if all markers provided the same type of information on polymorphism and genetic relationships among populations; otherwise, it would be necessary to use different markers to obtain the complete picture of the genetic structure of populations and species. In this study, we compared data of isozyme and RAPD markers in the populations of two tetraploid species of wild oats: Avena barbata populations collected in Argentina, and Avena murphyi populations collected in Spain and Morocco. The samples were evaluated for 9 isozymatic systems and 10 primers. The structure of genetic variability was studied using Nei's method, and the relationships between populations were estimated using Hedrick and Jaccard's similarities for isozymes and RAPDs, respectively. As expected, RAPDs were more polymorphic than isozymes, but the information obtained from both markers was weakly correlated. The various reasons for this observation are discussed, but our conclusion is that in order to study the structure of genetic variability, several types of markers should be used. PMID:12378251

Benchacho, Mohammed; Guma, Rosana; Pérez De La Vega, Marcelino; García, Pedro

2002-01-01

96

Use of three different marker systems to estimate genetic diversity of Indian elite rice varieties.  

PubMed

Genetic diversity among 42 Indian elite rice varieties, which is important for selection of parents for conventional breeding and hybrid program, was evaluated using three different types of DNA markers and parentage analysis. Random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and sequence tagged microsatellite site (STMS) markers resulted in mean heterozygosity values of 0.429, 0.675 and 0.882 over all loci, respectively, and marker index values of 2.21, 4.05 and 5.49, respectively. The three molecular marker systems together provide wider genome coverage and, therefore, would be a better indicator of the genetic relationships among the 42 elite rice cultivars than those revealed using individual molecular markers. A total of 153 bands (91%) were polymorphic out of 168 bands amplified, considering all the markers together. The average genetic similarity coefficient across all the 861 cultivar pairs was 0.70 while the average coefficient of parentage was 0.10. Cluster analysis revealed that there was a very poor correlation (correlation coefficient <0.1) between dendrograms generated using coefficients of parentage and molecular marker generated genetic similarities, which can be attributed to selection pressure, genetic drift, sampling of loci and unknown relationships among supposedly unrelated ancestors. PMID:11294614

Davierwala, A P; Chowdari, K V; Kumar, S; Reddy, A P; Ranjekar, P K; Gupta, V S

2000-01-01

97

Development and genetic mapping of microsatellite markers from genome survey sequences in Brassica napus  

Microsoft Academic Search

Microsatellite or simple sequence repeat (SSR) markers are routinely used for tagging genes and assessing genetic diversity.\\u000a In spite of their importance, there are limited numbers of SSR markers available for Brassica crops. A total of 627 new SSR markers (designated BnGMS) were developed based on publicly available genome survey sequences\\u000a and used to survey polymorphisms among six B. napus

Xiaomao Cheng; Jinsong Xu; Shu Xia; Jianxun Gu; Yuan Yang; Jie Fu; Xiaoju Qian; Shunchang Zhang; Jiangsheng Wu; Kede Liu

2009-01-01

98

Consensus genetic structuring and typological value of markers using multiple co-inertia analysis  

Microsoft Academic Search

Working with weakly congruent markers means that consensus genetic structuring of populations requires methods explicitly devoted to this purpose. The method, which is presented here, belongs to the multivariate analyses. This method consists of different steps. First, single-marker analyses were performed using a version of principal component analysis, which is designed for allelic frequencies (%PCA). Drawing confidence ellipses around the

Denis Laloë; Thibaut Jombart; Anne-Béatrice Dufour; Katayoun Moazami-Goudarzi

2007-01-01

99

Genetic Linkage Maps of the Guppy ( Poecilia reticulata ): Assignment of RAPD Markers to Multipoint Linkage Groups  

Microsoft Academic Search

Genetic linkage maps of the guppy ( Poecilia reticulata) were constructed from independent crosses between the Tuxedo strain and a feral line (Wildtype). Segregation patterns of random amplified polymorphic DNA (RAPD) markers and phenotypic markers were investigated in F 2 offspring of Tuxedo ?? × Wildtype ?? and Wildtype ?? × Tuxedo ?? crosses. Among the 300 and 276 RAPD

Gideon Khoo; Meng Huat Lim; Haridas Suresh; Damien K. Y. Gan; Kok Fang Lim; Fan Chen; Woon-Khiong Chan; Tit Meng Lim; Violet P. E. Phang

2003-01-01

100

Cystic Fibrosis Locus Defined by a Genetically Linked Polymorphic DNA Marker  

Microsoft Academic Search

A polymorphic DNA marker has been found genetically linked, in a set of 39 human families, to an autosomal recessive gene that causes cystic fibrosis (CF), a disease affecting one in 2000 Caucasian children. The DNA marker (called D0CRI-917) is also linked to the PON locus, which by independent evidence is linked to the CF locus. The best estimates of

Lap-Chee Tsui; Manuel Buchwald; David Barker; Jeffrey C. Braman; Robert Knowlton; James W. Schumm; Hans Eiberg; Jan Mohr; Dara Kennedy; Natasa Plavsic; Martha Zsiga; Danuta Markiewicz; Gita Akots; Valerie Brown; Cynthia Helms; Thomas Gravius; Carol Parker; Kenneth Rediker; Helen Donis-Keller

1985-01-01

101

Construction of a genetic linkage map in the wild plant Mimulus using RAPD and isozyme markers  

Microsoft Academic Search

As a first step to mapping quantitative trait loci for mating system differences, a genetic linkage map was generated from an interspecific backcross between Mimulus guttatus and Mimulus platycalyx. The linkage map consists of 99 RAPD and two isozyme markers. Eighty-one of these markers were mapped to 15 linkage groups, spanning 1437 contiguous centiMorgans, and covering 58% of the estimated

Jing-Zhong Lin; Kermit Ritland

1996-01-01

102

A review on SNP and other types of molecular markers and their use in animal genetics  

Microsoft Academic Search

During the last ten years, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in animal genetics studies. Amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high

Alain Vignal; Denis Milan; Magali SanCristobal; André Eggen

2002-01-01

103

Genetic and Economic Analysis of a Targeted Marker-assisted Wheat Breeding Strategy  

Microsoft Academic Search

The advent of molecular markers as a tool to aid selection has provided plant breeders with the opportunity to rapidly deliver superior genetic solutions to problems in agricultural production systems. However, a major constraint to the implementation of marker-assisted selection (MAS) in pragmatic breeding programs in the past has been the perceived high relative cost of MAS compared to conventional

Haydn Kuchel; Guoyou Ye; Rebecca Fox; Stephen Jefferies

2005-01-01

104

Distribution of Genetic Marker Concentrations for Fecal Indicator Bacteria in Sewage and Animal Feces  

PubMed Central

Very little is known about the density and distribution of fecal indicator bacteria (FIB) genetic markers measured by quantitative real-time PCR (qPCR) in fecal pollution sources. Before qPCR-based FIB technologies can be applied to waste management and public health risk applications, it is vital to characterize the concentrations of these genetic markers in pollution sources (i.e., untreated wastewater and animal feces). We report the distribution of rRNA genetic markers for several general FIB groups, including Clostridium spp., Escherichia coli, enterococci, and Bacteroidales, as determined by qPCR on reference collections consisting of 54 primary influent sewage samples collected from treatment facilities across the United States and fecal samples representing 20 different animal species. Based on raw sewage sample collection data, individual FIB genetic markers exhibited a remarkable similarity in concentration estimates from locations across the United States ranging from Hawaii to Florida. However, there was no significant correlation between genetic markers for most FIB combinations (P > 0.05). In addition, large differences (up to 5 log10 copies) in the abundance of FIB genetic markers were observed between animal species, emphasizing the importance of indicator microorganism selection and animal source contribution for future FIB applications.

Kelty, Catherine A.; Varma, Manju; Sivaganesan, Mano; Haugland, Richard A.

2012-01-01

105

Distribution of genetic marker concentrations for fecal indicator bacteria in sewage and animal feces.  

PubMed

Very little is known about the density and distribution of fecal indicator bacteria (FIB) genetic markers measured by quantitative real-time PCR (qPCR) in fecal pollution sources. Before qPCR-based FIB technologies can be applied to waste management and public health risk applications, it is vital to characterize the concentrations of these genetic markers in pollution sources (i.e., untreated wastewater and animal feces). We report the distribution of rRNA genetic markers for several general FIB groups, including Clostridium spp., Escherichia coli, enterococci, and Bacteroidales, as determined by qPCR on reference collections consisting of 54 primary influent sewage samples collected from treatment facilities across the United States and fecal samples representing 20 different animal species. Based on raw sewage sample collection data, individual FIB genetic markers exhibited a remarkable similarity in concentration estimates from locations across the United States ranging from Hawaii to Florida. However, there was no significant correlation between genetic markers for most FIB combinations (P > 0.05). In addition, large differences (up to 5 log(10) copies) in the abundance of FIB genetic markers were observed between animal species, emphasizing the importance of indicator microorganism selection and animal source contribution for future FIB applications. PMID:22504809

Kelty, Catherine A; Varma, Manju; Sivaganesan, Mano; Haugland, Richard A; Shanks, Orin C

2012-06-01

106

Genetics  

MedlinePLUS

... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Genes are sections of DNA. ...

107

The Application and Performance of Single Nucleotide Polymorphism Markers for Population Genetic Analyses of Lepidoptera  

PubMed Central

Microsatellite markers are difficult to apply within lepidopteran studies due to the lack of locus-specific PCR amplification and the high proportion of “null” alleles, such that erroneous estimations of population genetic parameters often result. Herein single nucleotide polymorphism (SNP) markers are developed from Ostrinia nubilalis (Lepidoptera: Crambidae) using next generation expressed sequence tag (EST) data. A total of 2742 SNPs were predicted within a reference assembly of 7414 EST contigs, and a subset of 763 were incorporated into 24 multiplex PCR reactions. To validate this pipeline, 5 European and North American sample sites were genotyped at 178 SNP loci, which indicated 84 (47.2%) were in Hardy–Weinberg equilibrium. Locus-by-locus FST, analysis of molecular variance, and STRUCTURE analyses indicate significant genetic differentiation may exist between European and North American O. nubilalis. The observed genetic diversity was significantly lower among European sites, which may result from genetic drift, natural selection, a genetic bottleneck, or ascertainment bias due to North American origin of EST sequence data. SNPs are an abundant source of mutation data for molecular genetic marker development in non-model species, with shared ancestral SNPs showing application within closely related species. These markers offer advantages over microsatellite markers for genetic and genomic analyses of Lepidoptera, but the source of mutation data may affect the estimation of population parameters and likely need to be considered in the interpretation of empirical data.

Coates, Brad Steven; Bayles, Darrell O.; Wanner, Kevin W.; Robertson, Hugh M.; Hellmich, Richard L.; Sappington, Thomas W.

2011-01-01

108

Decay of genetic markers for fecal bacterial indicators and pathogens in sand from Lake Superior.  

PubMed

Beach sands impact water quality and pathogen loads, however, the comparative decay of the fecal indicator bacteria (FIB) Enterococcus spp. and Escherichia coli, and pathogens in freshwater sand have not been examined. In this study, freshwater sand microcosms were inoculated with sewage and pure cultures of bacterial pathogens to compare relative decay rates. The abundance of culturable Enterococcus spp. and E. coli, genetic markers for Enterococcus spp. (Entero1), total Bacteroides (AllBac), and human-specific Bacteroides (HF183), and genetic markers for the pathogens Campylobacter jejuni, methicillin-resistant Staphylococcus aureus (MRSA), Salmonella enterica subsp. enterica serovar Typhimurium, and Shigella flexneri were monitored over the course of two weeks using conventional culture methods and quantitative PCR (qPCR). The effect of moisture on the persistence of culturable FIB and all genetic markers was also determined. In addition, propidium monoazide (PMA) treatment was used to examine differences in the persistence of total genetic markers and those from live cells. Decay rates were statistically compared using Tukey's test. Moisture had a significant (p ? 0.05) effect on the decay rates of culturable indicator bacteria, total AllBac markers, and genetic markers for FIB, Salmonella, and MRSA from live cells. At 14% sand moisture, the decay rate of total markers was slower than that of live cells for all qPCR assays, but at 28% moisture, there was no difference in the decay rates of total and live markers for any assay. AllBac and MRSA markers increased in sand at 28% moisture, probably indicating cellular growth. Overall, culturable FIB and HF183 had decay rates that were most comparable to the bacterial pathogen markers examined in this study, whereas Entero1 and AllBac rarely exhibited decay rates similar to the bacterial pathogens in this study. The choice of FIB for assessment of fecal contamination in freshwater sand should take into account the pathogen of concern and sand moisture conditions. PMID:24793108

Eichmiller, Jessica J; Borchert, Andrew J; Sadowsky, Michael J; Hicks, Randall E

2014-08-01

109

Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers  

PubMed Central

Background Field pea (Pisum sativum L.) and faba bean (Vicia faba L.) are cool-season grain legume species that provide rich sources of food for humans and fodder for livestock. To date, both species have been relative 'genomic orphans' due to limited availability of genetic and genomic information. A significant enrichment of genomic resources is consequently required in order to understand the genetic architecture of important agronomic traits, and to support germplasm enhancement, genetic diversity, population structure and demographic studies. Results cDNA samples obtained from various tissue types of specific field pea and faba bean genotypes were sequenced using 454 Roche GS FLX Titanium technology. A total of 720,324 and 304,680 reads for field pea and faba bean, respectively, were de novo assembled to generate sets of 70,682 and 60,440 unigenes. Consensus sequences were compared against the genome of the model legume species Medicago truncatula Gaertn., as well as that of the more distantly related, but better-characterised genome of Arabidopsis thaliana L.. In comparison to M. truncatula coding sequences, 11,737 and 10,179 unique hits were obtained from field pea and faba bean. Totals of 22,057 field pea and 18,052 faba bean unigenes were subsequently annotated from GenBank. Comparison to the genome of soybean (Glycine max L.) resulted in 19,451 unique hits for field pea and 16,497 unique hits for faba bean, corresponding to c. 35% and 30% of the known gene space, respectively. Simple sequence repeat (SSR)-containing expressed sequence tags (ESTs) were identified from consensus sequences, and totals of 2,397 and 802 primer pairs were designed for field pea and faba bean. Subsets of 96 EST-SSR markers were screened for validation across modest panels of field pea and faba bean cultivars, as well as related non-domesticated species. For field pea, 86 primer pairs successfully obtained amplification products from one or more template genotypes, of which 59% revealed polymorphism between 6 genotypes. In the case of faba bean, 81 primer pairs displayed successful amplification, of which 48% detected polymorphism. Conclusions The generation of EST datasets for field pea and faba bean has permitted effective unigene identification and functional sequence annotation. EST-SSR loci were detected at incidences of 14-17%, permitting design of comprehensive sets of primer pairs. The subsets from these primer pairs proved highly useful for polymorphism detection within Pisum and Vicia germplasm.

2012-01-01

110

An annotated genetic map of loblolly pine based on microsatellite and cDNA markers  

PubMed Central

Background Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map. Results The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM(Kosambi) across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs) and 149 were from non-transcribed genomic sequences (genomic-SSRs). Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO) terms. Duplicate (i.e., redundant accessory) and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, He, among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap. Conclusions Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped genes with UniGene clusters and GO terms allowed assessment of redundant and paralogous EST markers and further improved the quality and utility of the genetic map for P. taeda.

2011-01-01

111

Analysis of randomly amplified polymorphic DNA (RAPD) for identifying genetic markers associated with canine hip dysplasia  

Microsoft Academic Search

Canine hip dysplasia is a heritable developmental disease resulting, in part, from increased laxity in hip joints and is a precursor to degenerative joint disease. Iden- tification of genetic markers linked to joint laxity would foster development of more accurate diagnostic methods, facilitate identification of the disease gene(s), and supplement efforts to establish physical\\/genetic maps of the canine genome. Work

X. Wang; A. B. Miller; A. J. Lepine; J. D. Scott; K. E. Murphy

1999-01-01

112

Map Error Reduction: Using Genetic and Sequence-Based Physical Maps to Order Closely Linked Markers  

Microsoft Academic Search

The Marshfield comprehensive genetic maps are frequently used for linkage and association studies, however, for some regions of these maps the marker order has low level of likelihood ratio support. In order to investigate the level of statistical support and the accuracy of the genetic maps compared to sequence-based physical maps, two ?30 cM autosomal regions were selected. The first

Andrew T. DeWan; Antonio R. Parrado; Tara C. Matise; Suzanne M. Leal

2002-01-01

113

Genetic Diversity Analysis of Faba Bean ( Vicia faba L.) Based on EST-SSR Markers  

Microsoft Academic Search

Faba bean (Vicia faba L.), one of the most important legumes in the world, evolved different types of cultivars due to its partial cross-pollination. The development of simple sequence repeat (SSR) markers from expressed sequence tags (EST) provided a useful tool for investigation of its genetic diversity. The purpose of the present study was to investigate the genetic diversity of

Ya-ming GONG; Sheng-chun XU; Wei-hua MAO; Ze-yun LI; Qi-zan HU; Gu-wen ZHANG; Ju DING

2011-01-01

114

Genetic diversity of bitter gourd ( Momordica charantia L.) genotypes revealed by RAPD markers and agronomic traits  

Microsoft Academic Search

Bitter gourd or bitter melon (Momordica charantia L.) is considered as minor cucurbitaceous vegetable in spite of having considerable nutritional and medicinal properties. Although some reports on genetic diversity based on morphological characterization are available, no work has been conducted to estimate genetic diversity using molecular markers in this crop. In the present study, 38 genotypes of M. charantia including

S. S. Dey; A. K. Singh; D. Chandel; T. K. Behera

2006-01-01

115

Genetic Stock Identification of Steelhead in the Columbia River Basin: An Evaluation of Different Molecular Markers  

Microsoft Academic Search

Protein genetic markers (allozymes) have been used during the last decade in a genetic stock identification (GSI) program by state and federal management agencies to monitor stocks of steelhead Oncorhynchus mykiss in the Columbia River basin. In this paper we report new data for five microsatellite and three intron loci from 32 steelhead populations in the three upriver evolutionarily significant

Gary A. Winans; Melanie M. Paquin; Donald M. Van Doornik; Bruce M. Baker; Perry Thornton; Dan Rawding; Anne Marshall; Paul Moran; Steven Kalinowski

2004-01-01

116

Amplified Fragment Length Polymorphism Marker-Based Genetic Diversity in Tamarind (Tamarindus indica)  

Microsoft Academic Search

Tamarindus indica, commonly called tamarind, is a medium-sized evergreen tree that gives a high yield. The fruit is commonly used as a spice. Despite its commercial importance in the international market, it has been little explored. The genetic diversity and genetic relatedness of 36 tamarind genotypes were studied using amplified fragment length polymorphism (AFLP) markers. Twelve primer pairs were used

Ali Qaid Ahmed Yahya Algabal; Narayanaswamy Papanna; Luke Simon

2011-01-01

117

Potential of marker-assisted selection in hemp genetic improvement  

Microsoft Academic Search

Summary  The development and applications of molecular markers to hemp breeding are recent, dating back only to the mid-1990s. The main achievements in this field are reviewed. The analysis of Cannabis germplasm by RAPD, AFLP and microsatellites is discussed, with its consequence for the still debated species concept in Cannabis. DNA-based markers have also been exploited in the field of forensic

G. Mandolino; A. Carboni

2004-01-01

118

Genetic Biodiversity of Italian Olives (Olea europaea) Germplasm Analyzed by SSR Markers  

PubMed Central

The olive is an important fruit species cultivated for oil and table olives in Italy and the Mediterranean basin. The conservation of cultivated plants in ex situ collections is essential for the optimal management and use of their genetic resources. The largest ex situ olive germplasm collection consists of approximately 500 Italian olive varieties and corresponding to 85% of the total Italian olive germplasm is maintained at the Consiglio per la Ricerca e sperimentazione per l'Agricoltura, Centro di Ricerca per l'Olivicoltura e l'Industria Olearia (CRA-OLI), in Italy. In this work, eleven preselected nuclear microsatellite markers were used to assess genetic diversity, population structure, and gene flows with the aim of assembling a core collection. The dendrogram obtained utilizing the unweighted pair group method highlights the presence of homonymy and synonymy in olive tree datasets analyzed in this study. 439 different unique genotype profiles were obtained with this combination of 11 loci nSSR, representing 89.8% of the varieties analyzed. The remaining 10.2% comprises different variety pairs in which both accessions are genetically indistinguishable. Clustering analysis performed using BAPS software detected seven groups in Italian olive germplasm and gene flows were determined among identified clusters. We proposed an Italian core collection of 23 olive varieties capturing all detected alleles at microsatellites. The information collected in this study regarding the CRA-OLI ex situ collection can be used for breeding programs, for germplasm conservation, and for optimizing a strategy for the management of olive gene pools.

Vendramin, Giuseppe Giovanni; Chiappetta, Adriana

2014-01-01

119

Genetic biodiversity of Italian olives (Olea europaea) germplasm analyzed by SSR markers.  

PubMed

The olive is an important fruit species cultivated for oil and table olives in Italy and the Mediterranean basin. The conservation of cultivated plants in ex situ collections is essential for the optimal management and use of their genetic resources. The largest ex situ olive germplasm collection consists of approximately 500 Italian olive varieties and corresponding to 85% of the total Italian olive germplasm is maintained at the Consiglio per la Ricerca e sperimentazione per l'Agricoltura, Centro di Ricerca per l'Olivicoltura e l'Industria Olearia (CRA-OLI), in Italy. In this work, eleven preselected nuclear microsatellite markers were used to assess genetic diversity, population structure, and gene flows with the aim of assembling a core collection. The dendrogram obtained utilizing the unweighted pair group method highlights the presence of homonymy and synonymy in olive tree datasets analyzed in this study. 439 different unique genotype profiles were obtained with this combination of 11 loci nSSR, representing 89.8% of the varieties analyzed. The remaining 10.2% comprises different variety pairs in which both accessions are genetically indistinguishable. Clustering analysis performed using BAPS software detected seven groups in Italian olive germplasm and gene flows were determined among identified clusters. We proposed an Italian core collection of 23 olive varieties capturing all detected alleles at microsatellites. The information collected in this study regarding the CRA-OLI ex situ collection can be used for breeding programs, for germplasm conservation, and for optimizing a strategy for the management of olive gene pools. PMID:24723801

Muzzalupo, Innocenzo; Vendramin, Giuseppe Giovanni; Chiappetta, Adriana

2014-01-01

120

A novel set of single-copy nuclear DNA markers for the genetic study of Salicaceae.  

PubMed

Species of Populus are widely distributed worldwide, playing a significant role in both ecology and economy. However, the lack of single-copy nuclear markers limits knowledge about the phylogeny and population genetics of this genus. In the present study, primer pairs of 15 single-copy nuclear markers were developed through bioinformatic methods based on complete genomic sequences of Populus trichocarpa and Salix arbutifolia. Twenty individuals of Populus davidiana Dode and Salix matsudana Koidz were used to evaluate the basic application of these markers with respect to marker length and diversity indices, respectively. The utility of single-copy nuclear markers is anticipated to facilitate further studies about the phylogeny, population genetics, and phylogeography of this genus, in addition to providing information about the evolutionary dynamics of Salicaceae. PMID:25062424

Du, S H; Wang, Z S; Zhang, J G

2014-01-01

121

Genetic diversity in Elymus caninus as revealed by isozyme, RAPD, and microsatellite markers.  

PubMed

Genetic diversity of 33 Elymus caninus accessions was investigated using isozyme, RAPD, and microsatellite markers. The three assays differed in the amount of polymorphism detected. Microsatellites detected the highest polymorphism. Six microsatellite primer pairs generated a total of 74 polymorphic bands (alleles), with an average of 15.7 bands per primer pair. Three genetic similarity matrices were estimated based on band presence or absence. Genetic diversity trees (dendrograms) were derived from each marker technique, and compared using Mantel's test. The correlation coefficients were 0.204, 0.267, and 0.164 between isozyme and RAPD distance matrices, RAPD and microsatellite distance matrices, and between isozyme and microsatellite distance matrices, respectively. The three methodologies gave differing views of the amount of variation present but all showed a high level of genetic variation in E. caninus. The following points may be drawn from this study whether based on RAPD, microsatellite, or isozyme data: (i) The Icelandic populations are consistently revealed by the three dendrograms. The congruence of the discrimination of this accession group by RAPD, microsatellite, and isozyme markers suggests that geographic isolation strongly influenced the evolution of the populations; (ii) The degree of genetic variation within accessions was notably great; and (iii) The DNA-based markers will be the more useful ones in detecting genetic diversity in closely related accessions. In addition, a dendrogram, which took into account all fragments produced by isozymes, RAPDs, and microsatellites, reflected better the relationships than did dendrograms based on only one type of marker. PMID:10382290

Sun, G L; Díaz, O; Salomon, B; von Bothmer, R

1999-06-01

122

Evaluation of the extent of genetic variability among Theobroma cacao accessions using RAPD and RFLP markers  

Microsoft Academic Search

Random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers were used to evaluate\\u000a genetic relationships within the Theobroma cacao species and to assess the organization of its genetic diversity. Genetic variability was estimated with 18 primers and 43\\u000a RFLP probes on 155 cocoa trees belonging to different morphological groups and coming from various geographic origins. The\\u000a majority

E. Lerceteau; T. Robert; V. Pétiard; D. Crouzillat

1997-01-01

123

Using genetic markers to orient the edges in quantitative trait networks: The NEO software  

Microsoft Academic Search

BACKGROUND: Systems genetic studies have been used to identify genetic loci that affect transcript abundances and clinical traits such as body weight. The pairwise correlations between gene expression traits and\\/or clinical traits can be used to define undirected trait networks. Several authors have argued that genetic markers (e.g expression quantitative trait loci, eQTLs) can serve as causal anchors for orienting

Jason E Aten; Tova F Fuller; Aldons J Lusis; Steve Horvath

2008-01-01

124

Electrophysiological markers of genetic risk for attention deficit hyperactivity disorder  

PubMed Central

Electroencephalography (EEG) is an ideal neuroscientific approach, providing a direct measurement of neural activity that demonstrates reliability, developmental stability and high heritability. This systematic review of a subset of domains evaluates the utility of electrophysiological measures as potential intermediate phenotypes for ADHD in the domains of quantitative EEG indices of arousal and intra-individual variability, and functional investigations of inhibitory and error processing using the event-related potential (ERP) technique. Each domain demonstrates consistent and meaningful associations with ADHD, a degree of genetic overlap with ADHD and potential links to specific genetic variants. Investigations of the genetic and environmental contributions to EEG/ERP and shared genetic overlap with ADHD may enhance molecular genetic studies and provide novel insights into aetiology. Such research will aid in the precise characterisation of the clinical deficits seen in ADHD and guide the development of novel intervention and prevention strategies for those at risk.

Tye, Charlotte; McLoughlin, Grainne; Kuntsi, Jonna; Asherson, Philip

2014-01-01

125

Consensus genetic structuring and typological value of markers using multiple co-inertia analysis  

PubMed Central

Working with weakly congruent markers means that consensus genetic structuring of populations requires methods explicitly devoted to this purpose. The method, which is presented here, belongs to the multivariate analyses. This method consists of different steps. First, single-marker analyses were performed using a version of principal component analysis, which is designed for allelic frequencies (%PCA). Drawing confidence ellipses around the population positions enhances %PCA plots. Second, a multiple co-inertia analysis (MCOA) was performed, which reveals the common features of single-marker analyses, builds a reference structure and makes it possible to compare single-marker structures with this reference through graphical tools. Finally, a typological value is provided for each marker. The typological value measures the efficiency of a marker to structure populations in the same way as other markers. In this study, we evaluate the interest and the efficiency of this method applied to a European and African bovine microsatellite data set. The typological value differs among markers, indicating that some markers are more efficient in displaying a consensus typology than others. Moreover, efficient markers in one collection of populations do not remain efficient in others. The number of markers used in a study is not a sufficient criterion to judge its reliability. "Quantity is not quality".

Laloe, Denis; Jombart, Thibaut; Dufour, Anne-Beatrice; Moazami-Goudarzi, Katayoun

2007-01-01

126

Genetic diversity in cultivated carioca common beans based on molecular marker analysis  

PubMed Central

A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats – SSRs and amplified fragment length polymorphisms – AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger’s modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.

Kupper Cardoso Perseguini, Juliana Morini; Chioratto, Alisson Fernando; Zucchi, Maria Imaculada; Colombo, Carlos Augusto; Carbonell, Sergio Augusto Moraes; Costa Mondego, Jorge Mauricio; Gazaffi, Rodrigo; Franco Garcia, Antonio Augusto; de Campos, Tatiana; de Souza, Anete Pereira; Rubiano, Luciana Benchimol

2011-01-01

127

The origin of the Japanese race based on genetic markers of immunoglobulin G  

PubMed Central

This review addresses the distribution of genetic markers of immunoglobulin G (Gm) among 130 Mongoloid populations in the world. These markers allowed the populations to be clearly divided into 2 groups, the northern and southern groups. The northern group is characterized by high frequencies of 2 marker genes, ag and ab3st, and an extremely low frequency of the marker gene afb1b3; and the southern group, in contrast, is indicated by a remarkably high frequency of afb1b3 and low frequencies of ag and ab3st. Based on the geographical distribution of the markers and gene flow of Gm ag and ab3st (northern Mongoloid marker genes) from northeast Asia to the Japanese archipelago, the Japanese population belongs basically to the northern Mongoloid group and is thus suggested to have originated in northeast Asia, most likely in the Baikal area of Siberia.

Matsumoto, Hideo

2009-01-01

128

Maximizing genetic differentiation in core collections by PCA-based clustering of molecular marker data.  

PubMed

Developing genetically diverse core sets is key to the effective management and use of crop genetic resources. Core selection increasingly uses molecular marker-based dissimilarity and clustering methods, under the implicit assumption that markers and genes of interest are genetically correlated. In practice, low marker densities mean that genome-wide correlations are mainly caused by genetic differentiation, rather than by physical linkage. Although of central concern, genetic differentiation per se is not specifically targeted by most commonly employed dissimilarity and clustering methods. Principal component analysis (PCA) on genotypic data is known to effectively describe the inter-locus correlations caused by differentiation, but to date there has been no evaluation of its application to core selection. Here, we explore PCA-based clustering of marker data as a basis for core selection, with the aim of demonstrating its use in capturing genetic differentiation in the data. Using simulated datasets, we show that replacing full-rank genotypic data by the subset of genetically significant PCs leads to better description of differentiation and improves assignment of genotypes to their population of origin. We test the effectiveness of differentiation as a criterion for the formation of core sets by applying a simple new PCA-based core selection method to simulated and actual data and comparing its performance to one of the best existing selection algorithms. We find that although gains in genetic diversity are generally modest, PCA-based core selection is equally effective at maximizing diversity at non-marker loci, while providing better representation of genetically differentiated groups. PMID:23178877

van Heerwaarden, Joost; Odong, T L; van Eeuwijk, F A

2013-03-01

129

Genetic diversity of spineless Cereus jamacaru accessions using morphological and molecular markers.  

PubMed

This is the first study to examine the genetic diversity of mandacaru cactus (Cereus jamacaru P. DC.). Plants of spineless mandacaru are commonly found in gardens and parks of urban areas in northeastern Brazil. In addition to exploring their ornamental potential, morphological, and genetic characterization may contribute to the development of plant materials that can be used as a source of macromolecules of potential economic interest. The goal of this study was to estimate the genetic variability of spineless mandacaru accessions using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) molecular markers, and to characterize their morphology. Ten samples of newly emitted shoots with differentiated areolas and ribs were collected from each accession from the Cactaceous Germplasm Collection of Embrapa Agroindústria Tropical, in Fortaleza, CE. Shoot shape and aspects of spine primordia (presence, location, grouping, and size of spines) were evaluated. The morphological analysis showed that the spineless mandacaru presented spine primordia. Twenty-six RAPD and 15 ISSR primers were polymorphic. A total of 262 markers were obtained, 129 of which were polymorphic. The average polymorphism of ISSR markers was higher than that of RAPD markers. The dendrograms for both analyses showed differentiation between accessions. Nevertheless, the molecular markers detected higher levels of diversity and a different pattern of diversity than those found using morphological markers. The molecular results revealed significant genetic variability both within and between groups. PMID:24222234

Oliveira, F I C; Bordallo, P N; Castro, A C R; Correia, D

2013-01-01

130

Combined Serological, Genetic, and Inflammatory Markers Differentiate Non-IBD, Crohn's Disease, and Ulcerative Colitis Patients  

PubMed Central

Background Previous studies have demonstrated that serological markers can assist in diagnosing inflammatory bowel disease (IBD). In this study, we aim to build a diagnostic tool incorporating serological markers, genetic variants, and markers of inflammation into a computational algorithm to examine patterns of combinations of markers to (1) identify patients with IBD and (2) differentiate patients with Crohn’s disease (CD) from ulcerative colitis (UC). Methods In this cross-sectional study, patient blood samples from 572 CD, 328 UC, 437 non-IBD controls, and 183 healthy controls from academic and community centers were analyzed for 17 markers: 8 serological markers (ASCA-IgA, ASCA-IgG, ANCA, pANCA, OmpC, CBir1, A4-Fla2, and FlaX), 4 genetic markers (ATG16L1, NKX2-3, ECM1, and STAT3), and 5 inflammatory markers (CRP, SAA, ICAM-1, VCAM-1, and VEGF). A diagnostic Random Forest algorithm was constructed to classify IBD, CD, and UC. Results Receiver operating characteristic analysis compared the diagnostic accuracy of using a panel of serological markers only (ASCA-IgA, ASCA-IgG, ANCA, pANCA, OmpC, and CBir1) versus using a marker panel that in addition to the serological markers mentioned above also included gene variants, inflammatory markers, and 2 additional serological markers (A4-Fla2 and FlaX). The extended marker panel increased the IBD versus non-IBD discrimination area under the curve from 0.80 (95% confidence interval [CI], ±0.05) to 0.87 (95% CI, ±0.04; P < 0.001). The CD versus UC discrimination increased from 0.78 (95% CI, ±0.06) to 0.93 (95% CI, ±0.04; P < 0.001). Conclusions Incorporating a combination of serological, genetic, and inflammation markers into a diagnostic algorithm improved the accuracy of identifying IBD and differentiating CD from UC versus using serological markers alone.

Plevy, Scott; Silverberg, Mark S.; Lockton, Steve; Stockfisch, Tom; Croner, Lisa; Stachelski, Jordan; Brown, Michelle; Triggs, Cheryl; Chuang, Emil; Princen, Fred; Singh, Sharat

2013-01-01

131

Genetic prognostic and predictive markers in colorectal cancer  

Microsoft Academic Search

Despite many studies of the likely survival outcome of individual patients with colorectal cancer, our knowledge of this subject remains poor. Until recently, we had virtually no understanding of individual responses to therapy, but the discovery of the KRAS mutation as a marker of probable failure of epidermal growth factor receptor (EGFR)-targeted therapy is a first step in the tailoring

Axel Walther; Elaine Johnstone; Charles Swanton; Rachel Midgley; Ian Tomlinson; David Kerr

2009-01-01

132

USING MOLECULAR MARKERS IN STUDY OF RICE GENETIC DIVERSITY  

Microsoft Academic Search

Random amplified polymorphism DNA (RAPD) was used as a DNA fingerprinting technique in rice germplasm evaluation. The high efficiency and random coverage of RADP markers were established to analyse the biodiversity of 72 rice germplasm accessions . We examined the amplification products in both their size and their polymorphism. Correlation matrix was carried out using the Genstat program. Cluster analysis

BUI CHI BUU; NGUYEN THI LANG

133

Imaging genetics of structural brain connectivity and neural integrity markers  

PubMed Central

We review studies that have used diffusion imaging (DI) and magnetic resonance spectroscopy (MRS) to investigate genetic associations. A brief description of the measures obtainable with these methods and of some methodological and interpretability limitations is given. The usefulness of DI and MRS in defining intermediate phenotypes and in demonstrating the effects of common genetic variants known to increase risk for psychiatric manifestations on anatomical and metabolic phenotypes are reviewed. The main focus is on schizophrenia where the greatest amount of data has been collected. Moreover, we present an example coming from a different approach, where the genetic alteration is known (the deletion that causes Williams syndrome) and the DI phenotype can shed new light on the function of genes affected by the mutation. We conclude that, although these are still early days of this type of research and many findings remain controversial, both techniques can significantly contribute to the understanding of genetic effects in the brain and the pathophysiology of psychiatric disorders.

Marenco, Stefano; Radulescu, Eugenia

2009-01-01

134

Merozoite surface protein-3 alpha as a genetic marker for epidemiologic studies in Plasmodium vivax: a cautionary note  

PubMed Central

Background Plasmodium vivax is the most widespread of the human malaria parasites in terms of geography, and is thought to present unique challenges to local efforts aimed at control and elimination. Parasite molecular markers can provide much needed data on P. vivax populations, but few such markers have been critically evaluated. One marker that has seen extensive use is the gene encoding merozoite surface protein 3-alpha (MSP-3?), a blood-stage antigen known to be highly variable among P. vivax isolates. Here, a sample of complete msp-3? gene sequences is analysed in order to assess its utility as a molecular marker for epidemiologic investigations. Methods Amplification, cloning and sequencing of additional P. vivax isolates from different geographic locations, including a set of Venezuelan field isolates (n?=?10), yielded a sample of 48 complete msp-3? coding sequences. Characterization of standard population genetic measures of diversity, phylogenetic analysis, and tests for recombination were performed. This allowed comparisons to patterns inferred from the in silico simulation of a polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) protocol used widely. Results The larger sample of MSP-3? diversity revealed incongruence between the observed levels of nucleotide polymorphism, which were high in all populations, and the pattern of PCR-RFLP haplotype diversity. Indeed, PCR-RFLP haplotypes were not informative of a population’s genetic diversity and identical haplotypes could be produced from analogous bands in the commonly used protocol. Evidence of frequent and variable insertion-deletion mutations and recurrent recombination between MSP-3? haplotypes complicated the inference of genetic diversity patterns and reduced the phylogenetic signal. Conclusions The genetic diversity of P. vivax msp-3? involves intragenic recombination events. Whereas the high genetic diversity of msp-3? makes it a promising marker for some epidemiological applications, the ability of msp-3? PCR-RFLP analysis to accurately track parasites is limited. Local studies of the circulating alleles are needed before implementing PCR-RFLP approaches. Furthermore, evidence from the global sample analysed here suggests such msp-3? PCR-RFLP methods are not suitable for broad geographic studies or tracking parasite populations for an extended period of time.

2013-01-01

135

Genetic characterization of Colombian Bahman cattle using microsatellites markers.  

PubMed

Genetic structure and diversity of 3789 animals of the Brahman breed from 23 Colombian regions were assessed. Considering the Brahman Zebu cattle as a single population, the multilocus test based on the HW equilibrium, shows significant differences (P < 0.001). Genetic characterization made on the cattle population allowed to examine the genetic variability, calculating a H(o) = 0.6621. Brahman population in Colombia was a small subdivision within populations (F(it) = 0.045), a geographic subdivision almost non-existent or low differentiation (F(st) = 0.003) and the F(is) calculated (0.042) indicates no detriment to the variability in the population, despite the narrow mating takes place or there is a force that causes the variability is sustained without inbreeding actually affect the cattle population. The outcomes of multivariate analyses, Bayesian inferences and interindividual genetic distances suggested that there is no genetic sub-structure in the population, because of the high rate of animal migration among regions. PMID:24450154

Gómez, Y M; Fernandez, M; Rivera, D; Gómez, G; Bernal, J E

2013-07-01

136

Evaluation of genetic diversity in Pampus argenteus using SSR markers.  

PubMed

In order to evaluate the germplasm resources of Pampus argenteus silver pomfret, the genetic diversity and population structure of 132 silver pomfret samples collected from the three regions (the East China Sea, the Yellow Sea and the Bohai Sea) were examined using 13 polymorphic microsatellite loci. Results indicated a high level of genetic diversity. The total number of observed alleles was 68, the mean allele number was 5.46 per locus, and the mean number of effective alleles was 4.91. The polymorphism information content ranged from 0.58 to 0.88. For the 13 polymorphic microsatellite loci, the results of analysis of molecular variance indicated that 92.45% of the genetic variation was contained within populations. Unweighted pair group method with arithmetic mean cluster analysis revealed significant genealogical branches or clusters corresponding to sampling localities. We concluded that there was high genetic diversity in these silver pomfret populations, and that this diversity was related to the complex environment. These results would contribute to important knowledge of genetic diversity and population structure, which would be crucial for establishing appropriate fishery management stocks for this species. PMID:24301952

Qin, Y; Shi, G; Sun, Y

2013-01-01

137

Use of Three Different Marker Systems to Estimate Genetic Diversity of Indian Elite Rice Varieties  

Microsoft Academic Search

Genetic diversity among 42 Indian elite rice varieties, which is important for selection of parents for conventional breeding\\u000a and hybrid program, was evaluated using three different types of DNA markers and parentage analysis. Random amplified polymorphic\\u000a DNA (RAPD), inter-simple sequence repeat (ISSR) and sequence tagged microsatellite site (STMS) markers resulted in mean heterozygosity\\u000a values of 0.429, 0.675 and 0.882 over

A. P. Davierwala; K. V. Chowdari; Shiv Kumar; A. P. K. Reddy; P. K. Ranjekar; V. S. Gupta

2000-01-01

138

Genetic Differentiation Among Goats Using Randomly Amplified Polymorphic DNA (RAPD) Markers  

Microsoft Academic Search

Anbarasan, K., Sharma, A.K., Singh, R.K., Deb, S.M. and Sharma, D. 2001. Genetic differentiation among goats using randomly amplified polymorphic DNA (RAPD) markers. J. Appl. Anim. Res., 20: 83–88.To develop population specific markers using randomly amplified polymorphic DNA—ploymerase chain reaction (RAPD—PCR) in meat (Black Bengal and Non-descript Rohilkhand Local), milk (Barbari) and pashmina (Chegu) producing goats, a total of 35

K. Anbarasan; A. K. Sharma; R. K. Singh; S. M. Deb; D. Sharma

2001-01-01

139

Contrasting genetic diversity relationships are revealed in rice (Oryza sativa L.) using different marker types  

Microsoft Academic Search

Genetic variation between samples of Oryza sativa from 19 localities in Bangladesh and Bhutan was assessed using two PCR-based molecular marker systems: RAPD (random amplification of polymorphic DNA) and ISSR-PCR (inter-simple sequence repeat polymerase chain reaction). Employing RAPD, a set of 14 decanucleotides of arbitrary sequence directed the amplification of 94 reproducible marker bands, 47 (50%) of which were polymorphic.

Beverley J. Parsons; H. John Newbury; Michael T. Jackson; Brian V. Ford-Lloyd

1997-01-01

140

Identification of genetic markers with synergistic survival effect in cancer  

PubMed Central

Background Cancers are complex diseases arising from accumulated genetic mutations that disrupt intracellular signaling networks. While several predisposing genetic mutations have been found, these individual mutations account only for a small fraction of cancer incidence and mortality. With large-scale measurement technologies, such as single nucleotide polymorphism (SNP) microarrays, it is now possible to identify combinatorial effects that have significant impact on cancer patient survival. Results The identification of synergetic functioning SNPs on genome-scale is a computationally daunting task and requires advanced algorithms. We introduce a novel algorithm, Geninter, to identify SNPs that have synergetic effect on survival of cancer patients. Using a large breast cancer cohort we generate a simulator that allows assessing reliability and accuracy of Geninter and logrank test, which is a standard statistical method to integrate genetic and survival data. Conclusions Our results show that Geninter outperforms the logrank test and is able to identify SNP-pairs with synergetic impact on survival.

2013-01-01

141

Collecting Duct Carcinomas Represent a Unique Tumor Entity Based on Genetic Alterations  

PubMed Central

Collecting duct carcinoma (CDC) is a rare renal neoplasm that is associated with poor prognosis due to its highly aggressive course and limited response to immuno- or chemotherapy. Histologically, CDC is defined as a subtype of renal cell carcinomas, but in some cases, it is difficult to differentiate from urothelial carcinomas (UC). Therefore the aim of this study was to determine genetic alterations of CDC in comparison to that of urothelial carcinomas of the upper urinary tract (UUT-UC) to clarify the histological origin of this rare tumor entity. Twenty-nine CDC samples were obtained from seven different German centers and compared with twenty-six urothelial carcinomas of the upper urinary tract. Comparative genomic hybridization (CGH) was used to investigate the genetic composition of patients’ tumors and allowed the detection of losses and gains of DNA copy numbers throughout the entire genome. The clinical data were correlated with CGH results. CGH analysis of CDC revealed DNA aberrations in many chromosomes. DNA losses were more frequently observed than gains, while high-level amplifications were not detected. The mean frequency of CDC chromosomal aberrations (4.9/case) was slightly lower than that in UUT-UC (5.4/case). Recurrent CDC DNA losses occurred at 8p (n=9/29), 16p (9/29), 1p (n=7/29) and 9p (n=7/29), and gains occurred in 13q (n=9/29). In contrast to CDC, the most frequently detected UUT-UC DNA aberration was a loss at 9q (n=13/26). DNA losses at 9q, 13q and 8q as well as gains at 8p showed significant variations in UUT-UC compared to CDC. There was no correlation between the patients’ clinical course and the presence or absence of these recurrent genetic alterations. CDCs are characterized by a different genetic pattern compared to UUT-UC. Regarding the published data on renal cell carcinoma, we conclude that CDC appears to be a unique entity among kidney carcinomas.

Parr, Martin; Hartmann, Arndt; Fussel, Susanne; Toma, Marieta; Grobholz, Rainer; Pflugmann, Thomas; Wullich, Bernd; Strauss, Arne; Behnes, Carl Ludwig; Otto, Wolfgang; Stockle, Michael; Jung, Volker

2013-01-01

142

Genetic linkage analysis of familial amyotrophic lateral sclerosis using human chromosome 21 microsatellite DNA markers.  

PubMed

Amyotrophic lateral sclerosis (ALS: Lou Gehrig's Disease) is a lethal neurodegenerative disease of upper and lower motorneurons in the brain and spinal cord. We previously reported linkage of a gene for familial ALS (FALS) to human chromosome 21 using 4 restriction fragment length polymorphism DNA markers [Siddique et al.: N Engl J Med 324:1381-1384, 1991] and identified disease-associated mutations in the superoxide dismutase (SOD)-1 gene in some ALS families [Rosen et al.: Nature 362:59-62, 1993]. We report here the genetic linkage data that led us to examine the SOD-1 gene for mutations. We also report a new microsatellite DNA marker for D21S63, derived from the cosmid PW517 [VanKeuren et al.: Am J Hum Genet 38:793-804, 1986]. Ten microsatellite DNA markers, including the new marker D21S63, were used to reinvestigate linkage of FALS to chromosome 21. Genetic linkage analysis performed with 13 ALS families for these 10 DNA markers confirmed the presence of a FALS gene on chromosome 21. The highest total 2-point LOD score for all families was 4.33, obtained at a distance of 10 cM from the marker D21S223. For 5 ALS families linked to chromosome 21, a peak 2-point LOD score of 5.94 was obtained at the DNA marker D21S223. A multipoint score of 6.50 was obtained with the markers D21S213, D21S223, D21S167, and FALS for 5 chromosome 21-linked ALS families. The haplotypes of these families for the 10 DNA markers revealed recombination events that further refined the location of the FALS gene to a segment of approximately 5 megabases (Mb) between D21S213 and D21S219.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7913294

Rosen, D R; Sapp, P; O'Regan, J; McKenna-Yasek, D; Schlumpf, K S; Haines, J L; Gusella, J F; Horvitz, H R; Brown, R H

1994-05-15

143

Finding Markers That Make a Difference: DNA Pooling and SNP-Arrays Identify Population Informative Markers for Genetic Stock Identification  

PubMed Central

Genetic stock identification (GSI) using molecular markers is an important tool for management of migratory species. Here, we tested a cost-effective alternative to individual genotyping, known as allelotyping, for identification of highly informative SNPs for accurate genetic stock identification. We estimated allele frequencies of 2880 SNPs from DNA pools of 23 Atlantic salmon populations using Illumina SNP-chip. We evaluated the performance of four common strategies (global FST, pairwise FST, Delta and outlier approach) for selection of the most informative set of SNPs and tested their effectiveness for GSI compared to random sets of SNP and microsatellite markers. For the majority of cases, SNPs selected using the outlier approach performed best followed by pairwise FST and Delta methods. Overall, the selection procedure reduced the number of SNPs required for accurate GSI by up to 53% compared with randomly chosen SNPs. However, GSI accuracy was more affected by populations in the ascertainment group rather than the ranking method itself. We demonstrated for the first time the compatibility of different large-scale SNP datasets by compiling the largest population genetic dataset for Atlantic salmon to date. Finally, we showed an excellent performance of our top SNPs on an independent set of populations covering the main European distribution range of Atlantic salmon. Taken together, we demonstrate how combination of DNA pooling and SNP arrays can be applied for conservation and management of salmonids as well as other species.

Ozerov, Mikhail; Vasemagi, Anti; Wennevik, Vidar; Diaz-Fernandez, Rogelio; Kent, Matthew; Gilbey, John; Prusov, Sergey; Niemela, Eero; Vaha, Juha-Pekka

2013-01-01

144

SEROLOGICAL AND BIOCHEMICAL GENETIC MARKERS AND THEIR ASSOCIATIONS WITH PSYCHIATRIC DISORDERS : A REVIEW  

PubMed Central

SUMMARY The studies pertaining to associations of serological and biochemical genetic markers (blood groups in particular and scrum proteins and enzymes in general) with the psychiatric disorders such as psychoses in general, Schizophrenia, manic-depressive psychosis including unipolar and bipolar affective disorders and neuroses have been critically examined. The reasons for inconsistent findings of various investigators have been pointed out to assist the future researchers to overcome the previous drawbacks. Implications of associations of genetic markers with the psychiatric disorders have been discussed and future areas of research suggested.

Balgir, R.S.

1983-01-01

145

Sodium-potassium cotransport activity as genetic marker in essential hypertension.  

PubMed Central

Sodium-potassium cotransport activity is thought to be defective in essential hypertension and could be a useful genetic marker for susceptibility to essential hypertension. In this study cotransport activity in subjects with hypertension was compared with that in normotensive controls. The effects of ethnic differences, environment, and antihypertensive drugs were also studied. Mean cotransport activity was lower in hypertensive subjects than in controls of the same ethnic groups. There was, however, a large overlap between controls and hypertensive subjects. No ethnic or environmental influences were found. The large overlap found suggests that sodium-potassium cotransport activity is not a useful genetic marker in essential hypertension.

Davidson, J S; Opie, L H; Keding, B

1982-01-01

146

Genetic analysis and marker assisted identification of life phases of red alga Gracilaria corticata (J. Agardh)  

Microsoft Academic Search

The present study firstly reports the cytological and molecular marker assisted differentiation of isomorphic population of\\u000a Gracilaria\\u000a corticata (J. Agardh) with inter and intra-phasic genetic diversity analysis using ISSR markers. The genetic diversity of inbreeding\\u000a population of G. corticata as determined in terms of percentage of polymorphic loci (PPL), average heterozygosity (He) and Shannon’s Weaver index (I)\\u000a were 59.80, 0.59

Ravi S. Baghel; Puja Kumari; A. J. Bijo; Vishal Gupta; C. R. K. Reddy; B. Jha

2011-01-01

147

Genetic Markers of Increased Susceptibility to Diabetic Nephropathy  

Microsoft Academic Search

The effect of exposure to diabetes on the kidney appears to be modulated by genetic factors determining a variable degree of susceptibility to diabetic nephropathy. Multiple loci are probably involved. Some of them might be found among the genes coding for components of the renin angiotensin system (renin, angiotensinogen, angiotensin I-converting enzyme, angiotensin receptors), some may regulate the way in

Alessandro Doria

1998-01-01

148

Genetic relationships among wild Felidae in Thailand using AFLP markers.  

PubMed

The cytogenetics of eight Felidae species in Thailand were investigated by the colchicines-hypotonic fixation-air drying technique followed by a conventional technique. All species studied have an identical number of 38 diploid chromosomes, indicating a close genetic relationship among species. At a deep study level, the genetic relationships of eight Felidae species were accessed by the AFLP method. Blood samples were collected from sources locating in their original regions for DNA extraction. With ten successful primer combinations, a total of 4208 scorable bands were generated. Of these bands, 18.91% are polymorphic. Percentages of Polymorphic Bands (PPB) for each primer combination range from 15.00 to 23.59%. The generating bands were used for dendrogram construction. The average genetic similarity values among all Felidae species are 68.20% (between Panthera tigris and Neofelis nebulosa) to 85.53% (between Prionailurus bengalensis and Prionailurus viverrinus). The dendrogram shows that the eight Felidae species were clustered together and the subfamily Pantherinae and Felinae with Neofelis nebulosa are distinguished. The Felinae, Prionailurus bengalensis, Prionailurus viverrinus, Catopuma temminckii, Felis chaus, Pardofelis marmorata and Neofelis nebulosa were clustered together with 91% bootstrap support and the Pantherinae, Panthera pardus is clustered with Panthera tigris with 92% bootstrap support. In summary, the ten successful primer combinations can be used to determine genetic differences among eight Thailand Felidae species. PMID:19070075

Srisamoot, Nattapong; Chaveerach, Arunrat; Nuchadomrong, Suporn; Sattayasai, Nison; Chaveerach, Prapansak; Tanomtong, Alongkoad; Pinthong, Krit

2007-08-15

149

PERMANENT GENETIC RESOURCES: Development of microsatellite markers for the guava rust fungus, Puccinia psidii.  

PubMed

We developed and characterized 15 polymorphic microsatellite markers present in the genome of the guava rust fungus, Puccinia psidii. The primers for these microsatellite markers were designed by sequencing clones from a genomic DNA library enriched for a simple sequence repeat (SSR) motif of (AG). All these 15 primer pairs successfully amplified DNA fragments from a sample of 22 P. psidii isolates, revealing a total of 71 alleles. The observed heterozygosity at the 15 loci ranged from 0.05 to 1.00. The SSR markers developed would be useful for population genetics study of the rust fungus. PMID:21585788

Zhong, Shaobin; Yang, Baojun; Alfenas, Acelino Couto

2008-03-01

150

Genetic diversity of Cosmos species revealed by RAPD and ISSR markers.  

PubMed

The genus Cosmos is native of America and is constituted by 34 species; 28 of them are endemic of Mexico. The cosmos are used as a nematicide, antimalarial, and antioxidative agent. The aim of this study was to estimate the genetic diversity among 7 cosmos species based on random amplified polymorphic DNA (RAPD) and inter-simple sequences repeats (ISSR) markers. With RAPD markers, the obtained polymorphism was 91.7 % and the genetic diversity was 0.33, whereas these values were 65.6%, and 0.22 from ISSR markers, respectively, indicating the presence of high genetic diversity among the Cosmos species that were analyzed. The unweighted pair group method with arithmetic mean dendrograms that were obtained with both markers were notably similar, revealing 2 clusters and indicating a clear genetic differentiation among the Cosmos species that were assessed. The first cluster comprised the species Cosmos sulphureus, Cosmos pacificus, and Cosmos diversifolius, while the second cluster included the species Cosmos purpureus, Cosmos crithmifolius, Cosmos bipinnatus, and Cosmos parviflorus. Besides this, the Cosmos species were clustered according to their collection sites. The Mantel test corroborates the correlation between the genetic distance and the geographic altitude of each Cosmos species. The results suggest that it is necessary to preserve the Cosmos species in their natural habitat in addition to the germoplasm collection for ex situ conservation. PMID:24338421

Rodríguez-Bernal, A; Piña-Escutia, J L; Vázquez-García, L M; Arzate-Fernández, A M

2013-01-01

151

Genetic diversity and relationships in mulberry (genus Morus) as revealed by RAPD and ISSR marker assays  

PubMed Central

Background The genus Morus, known as mulberry, is a dioecious and cross-pollinating plant that is the sole food for the domesticated silkworm, Bombyx mori. Traditional methods using morphological traits for classification are largely unsuccessful in establishing the diversity and relationships among different mulberry species because of environmental influence on traits of interest. As a more robust alternative, PCR based marker assays including RAPD and ISSR were employed to study the genetic diversity and interrelationships among twelve domesticated and three wild mulberry species. Results RAPD analysis using 19 random primers generated 128 discrete markers ranging from 500–3000 bp in size. One-hundred-nineteen of these were polymorphic (92%), with an average of 6.26 markers per primer. Among these were a few putative species-specific amplification products which could be useful for germplasm classification and introgression studies. The ISSR analysis employed six anchored primers, 4 of which generated 93 polymorphic markers with an average of 23.25 markers per primer. Cluster analysis of RAPD and ISSR data using the WINBOOT package to calculate the Dice coefficient resulted into two clusters, one comprising polyploid wild species and the other with domesticated (mostly diploid) species. Conclusion These results suggest that RAPD and ISSR markers are useful for mulberry genetic diversity analysis and germplasm characterization, and that putative species-specific markers may be obtained which can be converted to SCARs after further studies.

Awasthi, Arvind K; Nagaraja, GM; Naik, GV; Kanginakudru, Sriramana; Thangavelu, K; Nagaraju, Javaregowda

2004-01-01

152

[The systems of molecular genetic markers under cancer of stomach].  

PubMed

The study was organized to investigate the anomalous methylation of genes NA?1, RASSF1A, MLH1, N33, DAPK, the expression of genes hTERT. metalloproteinase MMP7, MMP9, survivin. COX-2, p53. The activity of telomerase in 106 samples of stomach tumors taken through intra-operation way and 53 samples of stomach tumors taken through endoscopic way and 50 samples of biopsy taken from patients with chronic calculous cholecystitis (comparison group) was analyzed too. These changes can be used as additional markers both in diagnostic of cancer of stomach and dynamic monitoring of operated patients. PMID:24640104

Nemtsova, M V; Bykov, I I; Tchekinova, N V; Zaletaev, D V; Glikhov, A I; Khorobrykh, T V

2013-11-01

153

Genetic diversity of functional food species Spinacia oleracea L. by protein markers.  

PubMed

Exploration of genetic diversity contributes primarily towards crop improvement. Spinaciaoleracea L. is a functional food species but unfortunately the genetic diversity of this vegetable is still unexplored. Therefore, this research was planned to explore the genetic diversity of S. oleracea by using morphological and protein markers. Protein profile of 25 accessions was generated on sodium dodecyl sulphate polyacrylamide gel. Total allelic variation of 27 bands was found. Out of these, 20 were polymorphic and the rest of the bands were monomorphic. Molecular weights of the bands ranged from 12.6 to 91.2 kDa. Major genetic differences were observed in accession 20541 (Peshawar) followed by 20180 (Lahore) and 19902 (AVRDC). Significant differences exist in the protein banding pattern. This variation can further be studied by advanced molecular techniques, including two-dimensional electrophoresis and DNA markers. PMID:24499432

Rashid, M; Yousaf, Z; Haider, M S; Khalid, S; Rehman, H A; Younas, A; Arif, A

2014-01-01

154

Genetic characterization of Iranian safflower (Carthamus tinctorius) using inter simple sequence repeats (ISSR) markers.  

PubMed

Safflower (Carthamus tinctorious L.) is valued as a source of high quality vegetable oil. 20 ISSR primers were used to assess the genetic diversity of 18 accessions of safflower collected from different geographical regions of Iran. The ISSR primers combinations revealed 57.6 % polymorphism, among 338 genetic loci amplified from the accessions. The sum of effective number of alleles and observed number of alleles were 29.76 and 36.77, respectively. To understand genetic relationships among these cultivars, Jacquards' similarity coefficient and UPGMA clustering algorithm were applied to the ISSR marker data set. ISSR markers grouped accessions into two main clusters and four sub clusters. Also, the principal coordinate analysis (PCoA) supported the cluster analysis results. The results showed these genotypes have high genetic diversity, and can be used for alternative safflower breeding program. PMID:24431491

Panahi, Bahman; Ghorbanzadeh Neghab, Mahmoud

2013-04-01

155

Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae  

PubMed Central

Background The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs), will facilitate genetics and breeding of carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development of 300 carrot SSR markers and their characterization at various levels. Results Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1%) were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F2 populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F2, allowing the genetic mapping of 55 SSRs (38 codominant) onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs), with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 D. carota accessions revealed a high level of polymorphism for these selected loci, with an average of 19 alleles/locus and 0.84 expected heterozygosity. Conclusions The addition of 55 SSRs to the carrot map, together with marker characterizations in six other mapping populations, will facilitate future comparative mapping studies and integration of carrot maps. The markers developed herein will be a valuable resource for assisting breeding, genetic, diversity, and genomic studies of carrot and other Apiaceae.

2011-01-01

156

Genetic Relationship of Curcuma Species from Northeast India Using PCR-Based Markers  

Microsoft Academic Search

Molecular genetic fingerprints of nine Curcuma species from Northeast India were developed using PCR-based markers. The aim involves elucidating there intra- and inter-specific\\u000a genetic diversity important for utilization, management, and conservation. Twelve random amplified polymorphic DNA (RAPD),\\u000a 19 Inter simple sequence repeats (ISSRs), and four amplified fragment length polymorphism (AFLP) primers produced 266 polymorphic\\u000a fragments. ISSR confirmed maximum polymorphism of

Archana Das; Vigya Kesari; Vinod M. Satyanarayana; Ajay Parida; Latha Rangan

2011-01-01

157

Impact of Mapped SSR Markers on the Genetic Diversity of Apricot ( Prunus armeniaca L.) in Tunisia  

Microsoft Academic Search

The impact of mapped microsatellites on the study of genetic diversity of Tunisian apricot accessions was assessed. The genetic\\u000a variability of 47 traditional apricot cultivars originating from several areas in Tunisia was investigated with 32 polymorphic\\u000a microsatellite loci selected for their location throughout the eight linkage groups of Prunus genome. The higher polymorphism and greater transportability of these markers among

Hedia Bourguiba; Lamia Krichen; Jean-Marc Audergon; Bouchaib Khadari; Neila Trifi-Farah

2010-01-01

158

Genetic alterations in medullary thyroid cancer: diagnostic and prognostic markers.  

PubMed

Medullary thyroid carcinoma (MTC) is a rare calcitonin producing neuroendocrine tumour that originates from the parafollicular C-cells of the thyroid gland. The RET proto-oncogene encodes the RET receptor tyrosine kinase, with consequently essential roles in cell survival, differentiation and proliferation. Somatic or germline mutations of the RET gene play an important role in this neoplasm in development of sporadic and familial forms, respectively. Genetic diagnosis has an important role in differentiating sporadic from familiar MTC. Furthermore, depending on the location of the mutation, patients can be classified into risk classes. Therefore, genetic screening of the RET gene plays a critical role not only in diagnosis but also in assessing the prognosis and course of MTC. PMID:22654561

A, Taccaliti; F, Silvetti; G, Palmonella; M, Boscaro

2011-12-01

159

Genetic Alterations in Medullary Thyroid Cancer: Diagnostic and Prognostic Markers  

PubMed Central

Medullary thyroid carcinoma (MTC) is a rare calcitonin producing neuroendocrine tumour that originates from the parafollicular C-cells of the thyroid gland. The RET proto-oncogene encodes the RET receptor tyrosine kinase, with consequently essential roles in cell survival, differentiation and proliferation. Somatic or germline mutations of the RET gene play an important role in this neoplasm in development of sporadic and familial forms, respectively. Genetic diagnosis has an important role in differentiating sporadic from familiar MTC. Furthermore, depending on the location of the mutation, patients can be classified into risk classes. Therefore, genetic screening of the RET gene plays a critical role not only in diagnosis but also in assessing the prognosis and course of MTC.

A, Taccaliti; F, Silvetti; G, Palmonella; M, Boscaro

2011-01-01

160

Chapter 10: Mining Genome-Wide Genetic Markers  

PubMed Central

Genome-wide association study (GWAS) aims to discover genetic factors underlying phenotypic traits. The large number of genetic factors poses both computational and statistical challenges. Various computational approaches have been developed for large scale GWAS. In this chapter, we will discuss several widely used computational approaches in GWAS. The following topics will be covered: (1) An introduction to the background of GWAS. (2) The existing computational approaches that are widely used in GWAS. This will cover single-locus, epistasis detection, and machine learning methods that have been recently developed in biology, statistic, and computer science communities. This part will be the main focus of this chapter. (3) The limitations of current approaches and future directions.

Zhang, Xiang; Huang, Shunping; Zhang, Zhaojun; Wang, Wei

2012-01-01

161

Genetic differentiation in Pyrenophora teres populations measured with AFLP markers.  

PubMed

The genetic structure and occurrence of mating types and forms of Pyrenophora teres, the causal agent of net blotch on barley, was studied among 278 isolates collected from the northern hemisphere and from Australia. Genetic differentiation was high (F(CT) 0.238, P=0.002) between P. teres f. teres (PTT) isolates originating from Northern Europe, North America, Russia and Australia. The P. teres population in Australia was clearly divided into two subgroups (F(CT) 0.793, P<0.001) according to the form identity: PTT and P. teres f. maculata (PTM), with the PTT samples showing a greater degree of differentiation (F(ST) 0.573, P<0.001) among Australian states than the PTM samples (F(CT) 0.219, P<0.001). No differentiation was found among locations within Australian states. Both mating types (MAT1 and MAT2) were equally common (1:1) in several locations in Australia and in Finland. The only exception was Krasnodar, Russia, where only MAT2 was identified. Our results show that the prevalence of sexual reproduction, occurrence of forms of P. teres, and genetic differentiation between geographical regions are highly variable. The paper discusses the various effects and outcomes of population selection in Australia and in the northern barley growing regions. PMID:17324759

Serenius, Marjo; Manninen, Outi; Wallwork, Hugh; Williams, Kevin

2007-02-01

162

Genetic Markers of Cardiovascular Disease in Rheumatoid Arthritis  

PubMed Central

Cardiovascular (CV) disease is the most common cause of premature mortality in patients with rheumatoid arthritis (RA). It is the result of an accelerated atherosclerotic process. Both RA and atherosclerosis are complex polygenic diseases. Besides traditional CV risk factors and chronic inflammation, a number of studies have confirmed the role of genetic factors in the development of the atherogenesis observed in RA. In this regard, besides a strong association between the HLA-DRB1?04 shared epitope alleles and both endothelial dysfunction, an early step in the atherosclerotic process, and clinically evident CV disease, other polymorphisms belonging to genes implicated in inflammatory and metabolic pathways, located inside and outside the HLA region, such as the 308 variant (G > A, rs1800629) of the TNFA locus, the rs1801131 polymorphism (A > C; position + 1298) of the MTHFR locus, or a deletion of 32 base pairs on the CCR5 gene, seem to be associated with the risk of CV disease in patients with RA. Despite considerable effort to decipher the genetic basis of CV disease in RA, further studies are required to better establish the genetic influence in the increased risk of CV events observed in patients with RA.

Rodriguez-Rodriguez, Luis; Lopez-Mejias, Raquel; Garcia-Bermudez, Mercedes; Gonzalez-Juanatey, Carlos; Gonzalez-Gay, Miguel A.; Martin, Javier

2012-01-01

163

Expanding Possibilities for Intervention against Small Ruminant Lentiviruses through Genetic Marker-Assisted Selective Breeding  

PubMed Central

Small ruminant lentiviruses include members that infect sheep (ovine lentivirus [OvLV]; also known as ovine progressive pneumonia virus/maedi-visna virus) and goats (caprine arthritis encephalitis virus [CAEV]). Breed differences in seroprevalence and proviral concentration of OvLV had suggested a strong genetic component in susceptibility to infection by OvLV in sheep. A genetic marker test for susceptibility to OvLV has been developed recently based on the TMEM154 gene with validation data from over 2,800 sheep representing nine cohorts. While no single genotype has been shown to have complete resistance to OvLV, consistent association in thousands of sheep from multiple breeds and management conditions highlight a new strategy for intervention by selective breeding. This genetic marker-assisted selection (MAS) has the potential to be a useful addition to existing viral control measures. Further, the discovery of multiple additional genomic regions associated with susceptibility to or control of OvLV suggests that additional genetic marker tests may be developed to extend the reach of MAS in the future. This review will cover the strengths and limitations of existing data from host genetics as an intervention and outline additional questions for future genetic research in sheep, goats, small ruminant lentiviruses, and their host-pathogen interactions.

White, Stephen N.; Knowles, Donald P.

2013-01-01

164

RAPD-SCAR marker and genetic relationship analysis of three Demodex species (Acari: Demodicidae).  

PubMed

For a long time, classification of Demodex mites has been mainly based on their hosts and phenotype characteristics. The study was the first to conduct molecular identification and genetic relationship analysis for six isolates of three Demodex species by random amplified polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR) marker. Totally, 239 DNA fragments were amplified from six Demodex isolates with 10 random primers in RAPD, of which 165 were polymorphic. Using a single primer, at least five fragments and at most 40 in the six isolates were amplified, whereas within a single isolate, a range of 35-49 fragments were amplified. DNA fingerprints of primers CZ 1-9 revealed intra- and interspecies difference in six Demodex isolates, whereas primer CZ 10 only revealed interspecies difference. The genetic distance and dendrogram showed the intraspecific genetic distances were closer than the interspecific genetic distances. The interspecific genetic distances of Demodex folliculorum and Demodex canis (0.7931-0.8140) were shorter than that of Demodex brevis and D. canis (0.8182-0.8987). The RAPD-SCAR marker displayed primer CZ 10 could be applied to identify the three Demodex species. The 479-bp fragment was specific for D. brevis, and the 261-bp fragment was specific for D. canis. The conclusion was that the RAPD-SCAR multi-marker was effective in molecular identification of three Demodex species. The genetic relationship between D. folliculorum and D. canis was nearer than that between D. folliculorum and D. brevis. PMID:22205351

Zhao, Ya-E; Wu, Li-Ping

2012-06-01

165

Genetic diversity in wild Dipsacus chinensis populations from China based on ISSR markers.  

PubMed

Wild Dipsacus chinensis plants in China have become endangered owing to over-harvesting and habitat fragmentation. We examined the genetic diversity and genetic structure of 90 individuals from three populations using inter-simple sequence repeat markers and found that 106 of 173 bands amplified by 22 informative and reliable primers were polymorphic. These findings correspond to a medium level of genetic diversity. At the species level, the estimates of parameters of genetic diversity were as follows: polymorphic loci (61.27%); effective number of alleles (1.3873); Nei's genetic diversity (0.2202); Shannon's information index (0.3235). At the population level, the estimates were polymorphic loci (9.53%); effective number of alleles (1.0419); Nei's genetic diversity (0.0258); Shannon's information index (0.0402). Nei's coefficient of genetic differentiation was 0.8829, which is consistent with Shannon's coefficient of genetic differentiation (0.8757). Most of the genetic variation existed among populations, and some differentiation may have resulted from habitat fragmentation and barriers to gene flow (gene flow = 0.0663). Combining our results with those of on-site field investigation, we conclude that the present genetic diversity and genetic structure of natural populations of D. chinensis have been strongly affected by harvesting and habitat fragmentation. We also propose strategies for the conservation of this plant. PMID:23661445

Chen, D-X; Li, L-Y; Zhang, X; Wang, Y; Zhang, Z

2013-01-01

166

Genetic relationships among wheat genotypes, as revealed by microsatellite markers and pedigree analysis.  

PubMed

Genetic relationships among 20 elite wheat genotypes were studied using microsatellite markers and pedigree analysis. A total of 93 polymorphic bands were obtained with 25 microsatellite primer pairs. Coefficient of parentage (COP) values were calculated using parentage information at the expansion level of 5. The pedigree-based similarity (mean 0.115, range 0.00-0.53) was lower than the similarity assessed using microsatellite markers (mean 0.70, range 0.47-0.91). Similarity estimates were used to construct dendrograms by using the unweighted pair-group method with arithmetic averages (UPGMA). Clustering of genotypes in respect of marker-based similarity revealed two groups. Genotype PBW442 diverged and appeared as distinct from all other genotypes in both marker-based and pedigree-based analysis. The correlation of COP values with genetic similarity values based on microsatellite markers is low (r = 0.285, p < 0.05). The results indicate a need to develop wheat varieties with a diverse genetic background and to incorporate new variability into the existing wheat gene pool. PMID:16278510

Sud, Suman; Bains, Navtej Singh; Nanda, Govinder Singh

2005-01-01

167

Genetic analysis and marker assisted identification of life phases of red alga Gracilaria corticata (J. Agardh).  

PubMed

The present study firstly reports the cytological and molecular marker assisted differentiation of isomorphic population of Gracilaria corticata (J. Agardh) with inter and intra-phasic genetic diversity analysis using ISSR markers. The genetic diversity of inbreeding population of G. corticata as determined in terms of percentage of polymorphic loci (PPL), average heterozygosity (He) and Shannon's Weaver index (I) were 59.80, 0.59 and 1.21, respectively. The inter-phasic pair-wise average polymorphism were found to be 31.6% between male and female, 24.0% in male and tetrasporophyte and 25.3% in female and tetrasporophyte. The intra-phasic average polymorphisms were calculated as a maximum of 5.5% between females, 4.2% between males and the lowest 2.4% between tetrasporophytes. The primer 10 generated a marker of 800 bp specific to male and 650 bp to female gametophyte, while the primer 17 generated a marker of 2,500 bp specific to tetrasporophyte. Both the UPGMA based dendrogram and PCA analysis clustered all the three life phases differentially as distinct identity. Cytological analysis by chromosome count revealed 24 chromosomes in both haploid male and female gametophytes (N) and 48 for diploid (2 N) tetrasporophyte further confirming their genetic distinctness. The life phase specific markers reported in this study could be of help in breeding programmes where differentiation of life phases at the early developmental stages is crucial. PMID:21116855

Baghel, Ravi S; Kumari, Puja; Bijo, A J; Gupta, Vishal; Reddy, C R K; Jha, B

2011-08-01

168

Comprehensive genetic discrimination of Leonurus cardiaca populations by AFLP, ISSR, RAPD and IRAP molecular markers.  

PubMed

Leonurus cardiaca is well known for its medicinal importance. In this investigation, genotypic characterization of this species from six eco-geographical regions of Iran was evaluated by four molecular techniques (AFLP, RAPD, ISSR and IRAP). A total of 899 polymorphic fragments were detected by used molecular markers (AFLP = 356, RAPD = 325, ISSR = 113 and IRAP = 105) with an overall average polymorphism of 81.24%. Genetic variation calculated using Shannon's Information index (I) and Nei's gene diversity index (H) showed high genetic diversity in studied germplasm. Also, analysis of molecular variance showed high genetic variation among (55%) and within populations (45%). UPGMA dendrogram constructed from combined data of molecular markers distinguished studied populations in accordance with the results obtained by each marker which all individuals were clearly differentiated into two major clusters. The correlation coefficients were statistically significant for all marker systems with the highest correlation between similarity matrixes of RAPD and ISSR markers (r = 0.82). The present results have an important implication for L. cardiaca germplasm characterization, improvement, and conservation. Furthermore, the characterized individuals exhibited a great deal of molecular variation and they seem to have a rich gene pool for breeding programs. PMID:24562682

Khadivi-Khub, Abdollah; Soorni, Aboozar

2014-06-01

169

Genetic diversity analysis of Bt cotton genotypes in Pakistan using simple sequence repeat markers.  

PubMed

The popularity of genetically modified insect resistant (Bt) cotton has promoted large scale monocultures, which is thought to worsen the problem of crop genetic homogeneity. Information on genetic diversity among Bt cotton varieties is lacking. We evaluated genetic divergence among 19 Bt cotton genotypes using simple sequence repeat (SSR) markers. Thirty-seven of 104 surveyed primers were found informative. Fifty-two primers selected on the basis of reported intra-hirsutum polymorphism in a cotton marker database showed a high degree of polymorphism, 56% compared to 13% for randomly selected primers. A total of 177 loci were amplified, with an average of 1.57 loci per primer, generating 38 markers. The amplicons ranged in size from 98 to 256 bp. The genetic similarities among the 19 genotypes ranged from 0.902 to 0.982, with an average of 0.947, revealing a lack of diversity. Similarities among genotypes from public sector organizations were higher than genotypes developed by private companies. Hybrids were found to be more distant compared to commercial cultivars and advanced breeding lines. Cluster analysis grouped the 19 Bt cotton genotypes into three major clusters and two independent entries. Cultivars IR-3701, Ali Akbar-802 and advanced breeding line VH-259 grouped in subcluster B2, with very narrow genetic distances despite dissimilar parentage. We found a very high level of similarity among Pakistani-bred Bt cotton varieties, which means that genetically diverse recurrent parents should be included to enhance genetic diversity. The intra-hirsutum polymorphic SSRs were found to be highly informative for molecular genetic diversity studies in these cotton varieties. PMID:22535395

Ullah, I; Iram, A; Iqbal, M Z; Nawaz, M; Hasni, S M; Jamil, S

2012-01-01

170

The Life of the Gay Gene: From Hypothetical Genetic Marker to Social Reality  

Microsoft Academic Search

The gay gene was first identified in 1993 as a correlation between the genetic marker Xq28 and gay male sexuality. The results of this original study were never replicated, and the biological reality of such an entity remains hypothetical. However, despite such tenuous provenance, the gay gene has persisted as a reference in science news, popular science writings, and in

Kate ORiordan

2012-01-01

171

A study of the genetical structure of the Cuban population: red cell and serum biochemical markers.  

PubMed Central

Gene frequencies of several red cell and serum gentic markers were determined in the three main racial groups--whites, mulattoes and Negroes--of the Cuban population. The results were used to estimate the relative contribution of Caucasian and Negro genes to the genetic makeup of these three groups and to calculate the frequencies of these genes in the general Cuban population.

Gonzalez, R; Ballester, J M; Estrada, M; Lima, F; Martinez, G; Wade, M; Colombo, B; Vento, R

1976-01-01

172

Genetic linkage mapping in peach using morphological, RFLP and RAPD markers  

Microsoft Academic Search

We have constructed a genetic linkage map of peach [Prunus persica (L.) Batsch] consisting of RFLP, RAPD and morphological markers, based on 71 F2 individuals derived from the self-fertilization of four F1 individuals of a cross between ‘New Jersey Pillar’ and KV 77119. This progeny, designated as the West Virginia (WV) family, segregates for genes controlling canopy shape, fruit flesh

S. Rajapakse; L. E. Belthoff; G. He; A. E. Estager; R. Scorza; I. Verde; R. E. Ballard; W. V. Baird; A. Callahan; R. Monet; A. G. Abbott

1995-01-01

173

Genetic analysis of two common carp broodstocks by RAPD and microsatellite markers  

Microsoft Academic Search

The whole broodstock of two Hungarian common carp farms—80 and 196 individuals—was analyzed by using random amplified polymorphic DNA (RAPD) assay and microsatellite analysis. Ten polymorphic RAPD markers and four microsatellites were selected to genotype both of the stocks. As expected, microsatellite analysis revealed more detailed information on genetic diversities than RAPD assay. Results obtained with both types of DNA

Richárd Bártfai; Sándor Egedi; Gen Hua Yue; Balázs Kovács; Béla Urbányi; Gizella Tamás; László Horváth; László Orbán

2003-01-01

174

Quantitative PCR for Detection and Enumeration of Genetic Markers of Bovine Fecal Pollution? †  

PubMed Central

Accurate assessment of health risks associated with bovine (cattle) fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for the detection of two recently described bovine feces-specific genetic markers and a method for the enumeration of these markers using a Markov chain Monte Carlo approach. Both assays exhibited a range of quantification from 25 to 2 × 106 copies of target DNA, with a coefficient of variation of <2.1%. One of these assays can be multiplexed with an internal amplification control to simultaneously detect the bovine-specific genetic target and presence of amplification inhibitors. The assays detected only cattle fecal specimens when tested against 204 fecal DNA extracts from 16 different animal species and also demonstrated a broad distribution among individual bovine samples (98 to 100%) collected from five geographically distinct locations. The abundance of each bovine-specific genetic marker was measured in 48 individual samples and compared to quantitative PCR-enumerated quantities of rRNA gene sequences representing total Bacteroidetes, Bacteroides thetaiotaomicron, and enterococci in the same specimens. Acceptable assay performance combined with the prevalence of DNA targets across different cattle populations provides experimental evidence that these quantitative assays will be useful in monitoring bovine fecal pollution in ambient waters.

Shanks, Orin C.; Atikovic, Emina; Blackwood, A. Denene; Lu, Jingrang; Noble, Rachel T.; Domingo, Jorge Santo; Seifring, Shawn; Sivaganesan, Mano; Haugland, Richard A.

2008-01-01

175

The Use of Incompletely Linked Markers in Genetic Counseling: Accuracy versus Linkage  

Microsoft Academic Search

The utility of incompletely linked, selectively neutral, multiallelic markers for tracing the transmission of associated genes is examined theoretically for all genetic counseling situations in which the diagnosis of deleterious progeny is in question. The analysis focuses on the fraction of progeny from each two locus mating which can be diagnosed with minimal accuracy A solely on the basis of

Marjorie A. Asmussen

1985-01-01

176

Genetic diversity analysis in Boerhavia diffusa L. of different geographic locations in India using RAPD markers  

Microsoft Academic Search

Boerhavia diffusa is extensively used in herbal medicines as well as in the Ayurvedic system, because it contains a set of clinically important compounds. In the present study, the genetic variability in Boerhavia diffusa between accessions of different geographical origin within the Indian territory is assessed through random amplified polymorphic DNA (RAPD) markers. Twenty-eight accessions of Boerhavia were screened with

Nidhi Shukla; N. S. Sangwan; H. O. Misra; R. S. Sangwan

2003-01-01

177

Genetic characterization of four strains of Nile tilapia (Oreochromis niloticus L.) using microsatellite markers.  

PubMed

Four domesticated strains of Nile tilapia (Oreochromis niloticus L.) were genetically characterized using 14 microsatellite markers and 64 animals per strain. Two strains, Chitralada (AIT) and International Development Research Centers (IDRC) were obtained from the AIT institute, Bangkok, Thailand. The GIFT strain (5th generation) came from NAGRI, Thailand, and the GOTT strain was supplied by the University of Göttingen, Germany. The average numbers of alleles per marker were 5.0 (GOTT), 5.4 (AIT), 5.6 (IDRC) and 7.5 (GIFT). Private alleles were found at all markers with the exception of two. No fixation of alleles was found at any marker. Population differentiation, FST, was 0.178 (great genetic differentiation) and confirmed grouping of the animals in strains. The expected level of heterozygosity ranged from 0.624 to 0.711, but the observed level of heterozygosity significantly deviated from the expected level in three strains. This was probably because of small population size. Moderate to great genetic differentiation was found between strains. A phylogenetic tree reflected the strains known histories. Application of the Weitzman approach showed that all strains have added value for the total genetic diversity and thus should be retained. PMID:15025567

Rutten, M J M; Komen, H; Deerenberg, R M; Siwek, M; Bovenhuis, H

2004-04-01

178

Analysis of genetic diversity in Ganoderma population with a novel molecular marker SRAP  

Microsoft Academic Search

Genetic marker technology designed to detect naturally occurring polymorphisms at the DNA level had become an invaluable and revolutionizing tool for both applied and basic studies of fungi. To eliminate the confusion on the taxonomy of Ganoderma strains, in this study, a collection of 31 accessions representative of morphotypes and some unclassified types was used for analyzing molecular diversity using

Shu-Jing Sun; Wei Gao; Shu-Qian Lin; Jian Zhu; Bao-Gui Xie; Zhi-Bin Lin

2006-01-01

179

On marker-assisted prediction of genetic value: beyond the ridge.  

PubMed Central

Marked-assisted genetic improvement of agricultural species exploits statistical dependencies in the joint distribution of marker genotypes and quantitative traits. An issue is how molecular (e.g., dense marker maps) and phenotypic information (e.g., some measure of yield in plants) is to be used for predicting the genetic value of candidates for selection. Multiple regression, selection index techniques, best linear unbiased prediction, and ridge regression of phenotypes on marker genotypes have been suggested, as well as more elaborate methods. Here, phenotype-marker associations are modeled hierarchically via multilevel models including chromosomal effects, a spatial covariance of marked effects within chromosomes, background genetic variability, and family heterogeneity. Lorenz curves and Gini coefficients are suggested for assessing the inequality of the contribution of different marked effects to genetic variability. Classical and Bayesian methods are presented. The Bayesian approach includes a Markov chain Monte Carlo implementation. The generality and flexibility of the Bayesian method is illustrated when a Lorenz curve is to be inferred.

Gianola, Daniel; Perez-Enciso, Miguel; Toro, Miguel A

2003-01-01

180

Cotransduction and Cotransformation of Genetic Markers in Bacillus Subtilis and Bacillus Licheniformis.  

National Technical Information Service (NTIS)

Bacteriophage SP-15, a large generalized transducing phage of Bacillus, was compared with phages PBS-1 and SP-10 for the ability to cotransduce pairs of genetic markers exhibiting different degrees of linkage. When auxotrophs of B. subtilis W-23 were used...

F. J. Tyeryar M. J. Taylor W. D. Lawton I. D. Goldberg

1969-01-01

181

Development of microsatellite markers in Cannabis sativa for DNA typing and genetic relatedness analyses  

Microsoft Academic Search

Microsatellite markers were developed for Cannabis sativa L. (marijuana) to be used for DNA typing (genotype identification) and to measure the genetic relationships between the different plants. Twelve different oligonucleotide probes were used to screen an enriched microsatellite library of Cannabis sativa in which 49% of the clones contained microsatellite sequences. Characterization of microsatellite loci in Cannabis revealed that GA\\/CT

H. J. Alghanim; J. R. Almirall

2003-01-01

182

Development and genetic mapping of microsatellite markers from genome survey sequences in Brassica napus.  

PubMed

Microsatellite or simple sequence repeat (SSR) markers are routinely used for tagging genes and assessing genetic diversity. In spite of their importance, there are limited numbers of SSR markers available for Brassica crops. A total of 627 new SSR markers (designated BnGMS) were developed based on publicly available genome survey sequences and used to survey polymorphisms among six B. napus cultivars that serve as parents for established populations. Among these SSR markers, 591 (94.3%) successfully amplified at least one fragment and 434 (73.4%) detected polymorphism among the six B. napus cultivars. No correlation was observed between SSR motifs, repeat number or repeat length with polymorphism levels. A linkage map was constructed using 163 newly developed BnGMS marker loci and anchored with 164 public SSRs in a doubled haploid population. These new markers are evenly distributed over all linkage groups (LGs). Given that the majority of these SSRs are derived from bacterial artificial chromosome (BAC) end sequences, they will be useful in the assignment of their cognate BACs to LGs and facilitate the integration of physical maps with genetic maps for genome sequencing in B. napus. PMID:19190889

Cheng, Xiaomao; Xu, Jinsong; Xia, Shu; Gu, Jianxun; Yang, Yuan; Fu, Jie; Qian, Xiaoju; Zhang, Shunchang; Wu, Jiangsheng; Liu, Kede

2009-04-01

183

Assessing Genetic Structure with Multiple Classes of Molecular Markers: A Case Study Involving the Introduced Fire Ant Solenopsis invicta  

Microsoft Academic Search

We used 30 genetic markers of 6 different classes to describe hierarchical genetic structure in introduced populations of the fire ant Solenopsis invicta. These included four classes of presumably neutral nuclear loci (allozymes, co- dominant random amplified polymorphic DNAs (RAPDs), microsatellites, and dominant RAPDs), a class comprising two linked protein-coding nuclear loci under selection, and a marker of the mitochondrial

Kenneth G. Ross; D. DeWayne Shoemaker; Michael J. B. Krieger; Christopher J. DeHeer; Laurent Keller

184

Common DNA Markers Can Account for More Than Half of the Genetic Influence on Cognitive Abilities  

PubMed Central

For nearly a century, twin and adoption studies have yielded substantial estimates of heritability for cognitive abilities, although it has proved difficult for genomewide-association studies to identify the genetic variants that account for this heritability (i.e., the missing-heritability problem). However, a new approach, genomewide complex-trait analysis (GCTA), forgoes the identification of individual variants to estimate the total heritability captured by common DNA markers on genotyping arrays. In the same sample of 3,154 pairs of 12-year-old twins, we directly compared twin-study heritability estimates for cognitive abilities (language, verbal, nonverbal, and general) with GCTA estimates captured by 1.7 million DNA markers. We found that DNA markers tagged by the array accounted for .66 of the estimated heritability, reaffirming that cognitive abilities are heritable. Larger sample sizes alone will be sufficient to identify many of the genetic variants that influence cognitive abilities.

Haworth, Claire M. A.; Meaburn, Emma L.; Price, Thomas S.; Davis, Oliver S. P.

2013-01-01

185

Dermatoglyphics: A genetic marker of early childhood caries.  

PubMed

Background: It is an accepted fact that genetics plays an important role in determination of palmar dermatoglyphic patterns. Since caries is a multifactorial disease with the influence of genetic pattern, this study was undertaken to explore the possibility of dermatoglyphics as a noninvasive and early predictor of dental caries in children, so as to initiate preventive oral health measures at an early age. Materials and Methods: The study group comprised of 200 children aged between 4 and 5 years. The dmfs score was evaluated. The experimental group (Group 1), comprised of 100 children with early childhood caries (ECC) with dmfs >5. The control group (Group 2) comprised of 100 children with dmfs score of 0. Results: An increased frequency of ulnar loops in caries-free children and whorls in children with ECC was observed. Low mean atd angle and low mean. Total ridge count was observed in the ECC group. Conclusion: There is definite variation in dermatoglyphics between the ECC and caries-free group, indicating that dermatoglyphic patterns can be used as a predictive tool for children with ECC. PMID:25001441

Anitha, C; Konde, Sapna; Raj, N Sunil; Kumar, N C; Peethamber, Preetha

2014-01-01

186

Genetic diversity in Spanish donkey breeds using microsatellite DNA markers  

PubMed Central

Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (HE) over all the populations varied between 0.637 and 0.684 in this study. The low GST value showed that only 3.6% of the diversity was between breeds (P < 0.01). Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, except HMS5 that showed agreement in all analysed populations. The cumulative exclusion probability (PE) was 0.999 in each breed, suggesting that the loci would be suitable for donkey parentage testing. The constructed dendrogram from the DA distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans.

Aranguren-Mendez, Jose; Jordana, Jordi; Gomez, Mariano

2001-01-01

187

Genetic marker anchoring by six-dimensional pools for development of a soybean physical map  

PubMed Central

Background Integrated genetic and physical maps are extremely valuable for genomic studies and as important references for assembling whole genome shotgun sequences. Screening of a BAC library using molecular markers is an indispensable procedure for integration of both physical and genetic maps of a genome. Molecular markers provide anchor points for integration of genetic and physical maps and also validate BAC contigs assembled based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy and an in silico approach to anchor molecular markers onto the soybean physical map. Results A total of 1,470 markers (580 SSRs and 890 STSs) were anchored by PCR on a subset of a Williams 82 BstY I BAC library pooled into 208 pools in six dimensions. This resulted in 7,463 clones (~1× genome equivalent) associated with 1470 markers, of which the majority of clones (6,157, 82.5%) were anchored by one marker and 1106 (17.5%) individual clones contained two or more markers. This contributed to 1184 contigs having anchor points through this 6-D pool screening effort. In parallel, the 21,700 soybean Unigene set from NCBI was used to perform in silico mapping on 80,700 Williams 82 BAC end sequences (BES). This in silico analysis yielded 9,835 positive results anchored by 4152 unigenes that contributed to 1305 contigs and 1624 singletons. Among the 1305 contigs, 305 have not been previously anchored by PCR. Therefore, 1489 (78.8%) of 1893 contigs are anchored with molecular markers. These results are being integrated with BAC fingerprints to assemble the BAC contigs. Ultimately, these efforts will lead to an integrated physical and genetic map resource. Conclusion We demonstrated that the six-dimensional soybean BAC pools can be efficiently used to anchor markers to soybean BACs despite the complexity of the soybean genome. In addition to anchoring markers, the 6-D pooling method was also effective for targeting BAC clones for investigating gene families and duplicated regions in the genome, as well as for extending physical map contigs.

Wu, Xiaolei; Zhong, Guohua; Findley, Seth D; Cregan, Perry; Stacey, Gary; Nguyen, Henry T

2008-01-01

188

Assessment of genetic diversity in the sorghum reference set using EST-SSR markers.  

PubMed

Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. In the present study, a reference set representing a wide range of sorghum genetic diversity was screened with 40 EST-SSR markers to validate both the use of these markers for genetic structure analyses and the population structure of this set. Grouping of accessions is identical in distance-based and model-based clustering methods. Genotypes were grouped primarily based on race within the geographic origins. Accessions derived from the African continent contributed 88.6 % of alleles confirming the African origin of sorghum. In total, 360 alleles were detected in the reference set with an average of 9 alleles per marker. The average PIC value was 0.5230 with a range of 0.1379-0.9483. Sub-race, guinea margaritiferum (Gma) from West Africa formed a separate cluster in close proximity to wild accessions suggesting that the Gma group represents an independent domestication event. Guineas from India and Western Africa formed two distinct clusters. Accessions belongs to the kafir race formed the most homogeneous group as observed in earlier studies. This analysis suggests that the EST-SSR markers used in the present study have greater discriminating power than the genomic SSRs. Genetic variance within the subpopulations was very high (71.7 %) suggesting that the germplasm lines included in the set are more diverse. Thus, this reference set representing the global germplasm is an ideal material for the breeding community, serving as a community resource for trait-specific allele mining as well as genome-wide association mapping. PMID:23708149

Ramu, P; Billot, C; Rami, J-F; Senthilvel, S; Upadhyaya, H D; Ananda Reddy, L; Hash, C T

2013-08-01

189

An integrated genetic and cytogenetic map for Zhikong scallop, Chlamys farreri, based on microsatellite markers.  

PubMed

The reliability of genome analysis and proficiency of genetic manipulation requires knowledge of the correspondence between the genetic and cytogenetic maps. In the present study, we integrated cytogenetic and microsatellite-based linkage maps for Zhikong scallop, Chlamys farreri. Thirty-eight marker-anchored BAC clones standing for the 19 linkage groups were used to be FISH probes. Of 38 BAC clones, 30 were successfully located on single chromosome by FISH and used to integrate the genetic and cytogenetic map. Among the 19 linkage groups, 12 linkage groups were physically anchored by 2 markers, 6 linkage groups were anchored by 1 marker, and one linkage group was not anchored any makers by FISH. In addition, using two-color FISH, six linkage groups were distinguished by different chromosomal location; linkage groups LG6 and LG16 were placed on chromosome 10, LG8 and LG18 on chromosome 14. As a result, 18 of 19 linkage groups were localized to 17 pairs of chromosomes of C. farreri. We first integrated genetic and cytogenetic map for C. farreri. These 30 chromosome specific BAC clones in the cytogenetic map could be used to identify chromosomes of C. farreri. The integrated map will greatly facilitate molecular genetic studies that will be helpful for breeding applications in C. farreri and the upcoming genome projects of this species. PMID:24705086

Feng, Liying; Hu, Liping; Fu, Xiaoteng; Liao, Huan; Li, Xuan; Zhan, Aibin; Zhang, Lingling; Wang, Shi; Huang, Xiaoting; Bao, Zhenmin

2014-01-01

190

Marker-based quantitative genetics in the wild?: the heritability and genetic correlation of chemical defenses in eucalyptus.  

PubMed

Marker-based methods for estimating heritability and genetic correlation in the wild have attracted interest because traditional methods may be impractical or introduce bias via G x E effects, mating system variation, and sampling effects. However, they have not been widely used, especially in plants. A regression-based approach, which uses a continuous measure of genetic relatedness, promises to be particularly appropriate for use in plants with mixed-mating systems and overlapping generations. Using this method, we found significant narrow-sense heritability of foliar defense chemicals in a natural population of Eucalyptus melliodora. We also demonstrated a genetic basis for the phenotypic correlation underlying an ecological example of conditioned flavor aversion involving different biosynthetic pathways. Our results revealed that heritability estimates depend on the spatial scale of the analysis in a way that offers insight into the distribution of genetic and environmental variance. This study is the first to successfully use a marker-based method to measure quantitative genetic parameters in a tree. We suggest that this method will prove to be a useful tool in other studies and offer some recommendations for future applications of the method. PMID:16143624

Andrew, R L; Peakall, R; Wallis, I R; Wood, J T; Knight, E J; Foley, W J

2005-12-01

191

Genetic markers and biomarkers for age-related macular degeneration  

PubMed Central

Age-related macular degeneration (AMD) is the leading cause of visual impairment and blindness in the USA. Although the treatment of AMD has evolved to include laser photocoagulation, photodynamic therapy, surgical macular translocation and antiangiogenesis agents, treatment options for advanced AMD are limited. Furthermore, the dry form of AMD, albeit less devastating than the wet form, has even fewer viable treatment options. This review summarizes the various biomarkers of AMD and analyzes whether or not they may one day be exploited to determine risks of disease onset, measure progression of disease or even assess the effects of treatment of AMD. Potential biomarkers are important to identify since some might be utilized to reflect the disease state of a particular patient and to individualize therapy. Although studies have yielded promising results for nutrient and inflammatory biomarkers, these results have been inconsistent. At present, the best available markers of AMD risk are single nucleotide polymorphisms (SNPs). SNPs in complement factor H (CFH) and PLEKHA1/ARMS2/HtrA1 capture a substantial fraction of AMD risk and permit the identification of individuals at high risk of developing AMD.

Ross, Robert J; Verma, Varun; Rosenberg, Kevin I; Chan, Chi-Chao; Tuo, Jingsheng

2007-01-01

192

Efficient genetic transformation of Sorghum using a visual screening marker.  

PubMed

To transform grain sorghum (Sorghum bicolor (L.) Moench) with a visual reporter gene (gfp) and a target gene (tlp), three genotypes (two inbreds, Tx 430 and C401, and a commercial hybrid, Pioneer 8505) were used. We obtained a total of 1011 fertile transgenic plants from 61 independent callus lines, which were produced from 2463 zygotic immature embryos via Agrobacterium-mediated transformation. The reporter gene, gfp, encoding green fluorescent protein (GFP), was used as a visual screening marker, and the target gene, tlp, encoding thaumatin-like protein (TLP), was chosen for enhancing resistance to fungal diseases and drought. Both genes were under the control of the maize ubi 1 promoter in the binary vector pPZP201. A total of 320 plants showing GFP expression, derived from 45 calli, were selected and analyzed by Southern blot analysis. There was a 100% correlation between the GFP expression and the presence of the target gene, tlp, in these plants. Transgenic plants showing strong TLP expression were confirmed by Western blotting with antiserum specific for TLP. The transgene segregated in various ratios among progeny, which was confirmed by examining seedlings showing GFP fluorescence. The progeny also showed different copy numbers of transgenics. This report describes the successful use of GFP screening for efficient production of stably transformed sorghum plants without using antibiotics or herbicides as selection agents. PMID:15838555

Gao, Zhensheng; Jayaraj, J; Muthukrishnan, S; Claflin, Larry; Liang, G H

2005-04-01

193

Population genetic data for 17 STR markers from Lebanon.  

PubMed

Seventeen autosomal STRs were analyzed (D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, CSF1PO, FGA, TH01, TPOX, vWA, Penta D, and Penta E) in the Lebanese population. A total of 192 unrelated individuals were genotyped for the 15 autosomal STRs in the Promega PowerPlex 16 STR kit. An additional 275 unrelated individuals were genotyped for the Applied Biosystems AmpFlSTR Identifiler and SGM+STR kits. Allele frequencies for the shared CODIS 13 loci among the three STR kits tested were not significantly different among individuals within the Lebanese population. Forensic and population genetic parameters for the 17 loci were calculated. We also compared the allele frequencies from this population with other populations in the same geographic vicinity. PMID:20863737

Chouery, Eliane; Coble, Michael D; Strouss, Katharine M; Saunier, Jessica L; Jalkh, Nadine; Medlej-Hashim, Myrna; Ayoub, Fouad; Mégarbané, André

2010-11-01

194

Genetic mapping of common buckwheat using DNA, protein and morphological markers.  

PubMed

Genetic mapping of F(2) progeny (n = 225) of hybrids between the Sobano variety of common buckwheat (Fagopyrum esculentum Moench) and the Homo wild accession (F. esculentum var. homotropicum) was carried out using randomly amplified polymorphic DNA (RAPD), sequence-tagged site (STS) and seed protein subunit markers, and three morphological traits. Ten linkage groups were identified, involving 87 RAPD markers, 12 STS markers, four seed protein subunit (PS(62)/PS(59), PS(49.8)/PS(51.4), PS(44)/PS(42.9), and PS(39.9)/PS(37.8)) markers, and three morphological alleles controlling homo/long style (H/s), shattering habit (Sht/sht), and acute/obtuse achene ridge (Ac/ac), covering a total of 655.2 cM. PMID:20416014

Pan, Shou-Ju; Chen, Qing-Fu

2010-02-01

195

Next generation DNA sequencing technology delivers valuable genetic markers for the genomic orphan legume species, Bituminaria bituminosa  

PubMed Central

Background Bituminaria bituminosa is a perennial legume species from the Canary Islands and Mediterranean region that has potential as a drought-tolerant pasture species and as a source of pharmaceutical compounds. Three botanical varieties have previously been identified in this species: albomarginata, bituminosa and crassiuscula. B. bituminosa can be considered a genomic 'orphan' species with very few genomic resources available. New DNA sequencing technologies provide an opportunity to develop high quality molecular markers for such orphan species. Results 432,306 mRNA molecules were sampled from a leaf transcriptome of a single B. bituminosa plant using Roche 454 pyrosequencing, resulting in an average read length of 345 bp (149.1 Mbp in total). Sequences were assembled into 3,838 isotigs/contigs representing putatively unique gene transcripts. Gene ontology descriptors were identified for 3,419 sequences. Raw sequence reads containing simple sequence repeat (SSR) motifs were identified, and 240 primer pairs flanking these motifs were designed. Of 87 primer pairs developed this way, 75 (86.2%) successfully amplified primarily single fragments by PCR. Fragment analysis using 20 primer pairs in 79 accessions of B. bituminosa detected 130 alleles at 21 SSR loci. Genetic diversity analyses confirmed that variation at these SSR loci accurately reflected known taxonomic relationships in original collections of B. bituminosa and provided additional evidence that a division of the botanical variety bituminosa into two according to geographical origin (Mediterranean region and Canary Islands) may be appropriate. Evidence of cross-pollination was also found between botanical varieties within a B. bituminosa breeding programme. Conclusions B. bituminosa can no longer be considered a genomic orphan species, having now a large (albeit incomplete) repertoire of expressed gene sequences that can serve as a resource for future genetic studies. This experimental approach was effective in developing codominant and polymorphic SSR markers for application in diverse genetic studies. These markers have already given new insight into genetic variation in B. bituminosa, providing evidence that a division of the botanical variety bituminosa may be appropriate. This approach is commended to those seeking to develop useful markers for genomic orphan species.

2011-01-01

196

The first genetic linkage map of Luohanguo (Siraitia grosvenorii ) based on ISSR and SRAP markers.  

PubMed

In this study, the first genetic map of Luohanguo (Siraitia grosvenorii (Swingle) C. Jeffrey) was constructed with 150 F? population individuals using inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. A total of 100 ISSRs and 196 SRAP primer combinations generated 51 and 222 polymorphic markers, respectively. Among the 273 markers obtained, 199 markers (29 ISSRs and 170 SRAPs) were mapped to 25 linkage groups. The map covered 1463.3 cM with a mean map distance of 7.35 cM between adjacent markers and a maximum map distance of 52.6 cM between two markers. The markers were distributed randomly in 25 groups except for minor clusters in the distal region of linkage groups. All 25 linkage groups consisted of 2-36 loci ranging in length from 19.5 to 152.6 cM and accounted for 59.8% of the total map distance. This map provides reference information for future molecular breeding work on Luohanguo. PMID:21217802

Liu, Lihua; Ma, Xiaojun; Wei, Jianhe; Qin, Jiaming; Mo, Changming

2011-01-01

197

Identifying genetic marker sets associated with phenotypes via an efficient adaptive score test  

PubMed Central

In recent years, genome-wide association studies (GWAS) and gene-expression profiling have generated a large number of valuable datasets for assessing how genetic variations are related to disease outcomes. With such datasets, it is often of interest to assess the overall effect of a set of genetic markers, assembled based on biological knowledge. Genetic marker-set analyses have been advocated as more reliable and powerful approaches compared with the traditional marginal approaches (Curtis and others, 2005. Pathways to the analysis of microarray data. TRENDS in Biotechnology 23, 429–435; Efroni and others, 2007. Identification of key processes underlying cancer phenotypes using biologic pathway analysis. PLoS One 2, 425). Procedures for testing the overall effect of a marker-set have been actively studied in recent years. For example, score tests derived under an Empirical Bayes (EB) framework (Liu and others, 2007. Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models. Biometrics 63, 1079–1088; Liu and others, 2008. Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models. BMC bioinformatics 9, 292–2; Wu and others, 2010. Powerful SNP-set analysis for case-control genome-wide association studies. American Journal of Human Genetics 86, 929) have been proposed as powerful alternatives to the standard Rao score test (Rao, 1948. Large sample tests of statistical hypotheses concerning several parameters with applications to problems of estimation. Mathematical Proceedings of the Cambridge Philosophical Society, 44, 50–57). The advantages of these EB-based tests are most apparent when the markers are correlated, due to the reduction in the degrees of freedom. In this paper, we propose an adaptive score test which up- or down-weights the contributions from each member of the marker-set based on the Z-scores of their effects. Such an adaptive procedure gains power over the existing procedures when the signal is sparse and the correlation among the markers is weak. By combining evidence from both the EB-based score test and the adaptive test, we further construct an omnibus test that attains good power in most settings. The null distributions of the proposed test statistics can be approximated well either via simple perturbation procedures or via distributional approximations. Through extensive simulation studies, we demonstrate that the proposed procedures perform well in finite samples. We apply the tests to a breast cancer genetic study to assess the overall effect of the FGFR2 gene on breast cancer risk.

Cai, Tianxi; Lin, Xihong; Carroll, Raymond J.

2012-01-01

198

Marker-Based Estimation of Genetic Parameters in Genomics  

PubMed Central

Linear mixed model (LMM) analysis has been recently used extensively for estimating additive genetic variances and narrow-sense heritability in many genomic studies. While the LMM analysis is computationally less intensive than the Bayesian algorithms, it remains infeasible for large-scale genomic data sets. In this paper, we advocate the use of a statistical procedure known as symmetric differences squared (SDS) as it may serve as a viable alternative when the LMM methods have difficulty or fail to work with large datasets. The SDS procedure is a general and computationally simple method based only on the least squares regression analysis. We carry out computer simulations and empirical analyses to compare the SDS procedure with two commonly used LMM-based procedures. Our results show that the SDS method is not as good as the LMM methods for small data sets, but it becomes progressively better and can match well with the precision of estimation by the LMM methods for data sets with large sample sizes. Its major advantage is that with larger and larger samples, it continues to work with the increasing precision of estimation while the commonly used LMM methods are no longer able to work under our current typical computing capacity. Thus, these results suggest that the SDS method can serve as a viable alternative particularly when analyzing ‘big’ genomic data sets.

Hu, Zhiqiu; Yang, Rong-Cai

2014-01-01

199

Markers  

ERIC Educational Resources Information Center

Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

Healthy Schools Network, Inc., 2011

2011-01-01

200

Genetic Characterization of the Gypsy Moth from China (Lepidoptera, Lymantriidae) Using Inter Simple Sequence Repeats Markers  

PubMed Central

This study provides the first genetic characterization of the gypsy moth from China (Lymantriadispar), one of the most recognized pests of forests and ornamental trees in the world. We assessed genetic diversity and structure in eight geographic populations of gypsy moths from China using five polymorphic Inter simple sequence repeat markers, which produced reproducible banding patterns. We observed 102 polymorphic loci across the 176 individuals sampled. Overall genetic diversity (Nei’s, H) was 0.2357, while the mean genetic diversity within geographic populations was 0.1845 ± 0.0150. The observed genetic distance among the eight populations ranged from 0.0432 to 0.1034. Clustering analysis (using an unweighted pair-group method with arithmetic mean and multidimensional scaling), revealed strong concordance between the strength of genetic relationships among populations and their geographic proximity. Analysis of molecular variance demonstrated that 25.43% of the total variability (FST = 0.2543, P < 0.001) was attributable to variation among geographic populations. The results of our analyses investigating the degree of polymorphism, genetic diversity (Nei’s and Shannon) and genetic structure, suggest that individuals from Hebei may be better able to adapt to different environments and to disperse to new habitats. This study provides crucial genetic information needed to assess the distribution and population dynamics of this important pest species of global concern.

Chen, Fang; Shi, Juan; Luo, You-qing; Sun, Shuang-yan; Pu, Min

2013-01-01

201

The genetic structure of adders (Vipera berus) in Fennoscandia: congruence between different kinds of genetic markers.  

PubMed

In order to elucidate the colonization history of Fennoscandian adders (Vipera berus), the phylogeographical patterns of two nuclear sets of DNA markers (random amplified polymorphic DNA and microsatellite) are compared with that previously obtained from mitochondrial DNA. An eastern and a western lineage within Fennoscandian adders is readily distinguishable using both sets of nuclear markers, corroborating the hypothesis that the lineages stem from separate glacial refugia. Moreover, the same contact zones as were derived from mitochondrial data are clearly identifiable. Both sets of nuclear markers detect a high level of admixture across one zone in northern Finland, with introgression reaching far west into Sweden. PMID:15367127

Carlsson, M; Söderberg, L; Tegelström, H

2004-10-01

202

Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow.  

PubMed

Neutral genetic markers are routinely used to define distinct units within species that warrant discrete management. Human-induced changes to gene flow however may reduce the power of such an approach. We tested the efficiency of adaptive versus neutral genetic markers in differentiating temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid high gene flow owing to artificial propagation and habitat alteration. We compared seven putative migration timing genes to ten microsatellite loci in delineating three migratory groups of Chinook in the Feather River, CA: offspring of fall-run hatchery broodstock that returned as adults to freshwater in fall (fall run), spring-run offspring that returned in spring (spring run), and fall-run offspring that returned in spring (FRS). We found evidence for significant differentiation between the fall and federally listed threatened spring groups based on divergence at three circadian clock genes (OtsClock1b, OmyFbxw11, and Omy1009UW), but not neutral markers. We thus demonstrate the importance of genetic marker choice in resolving complex life history types. These findings directly impact conservation management strategies and add to previous evidence from Pacific and Atlantic salmon indicating that circadian clock genes influence migration timing. PMID:24478800

O'Malley, Kathleen G; Jacobson, Dave P; Kurth, Ryon; Dill, Allen J; Banks, Michael A

2013-12-01

203

Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow  

PubMed Central

Neutral genetic markers are routinely used to define distinct units within species that warrant discrete management. Human-induced changes to gene flow however may reduce the power of such an approach. We tested the efficiency of adaptive versus neutral genetic markers in differentiating temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid high gene flow owing to artificial propagation and habitat alteration. We compared seven putative migration timing genes to ten microsatellite loci in delineating three migratory groups of Chinook in the Feather River, CA: offspring of fall-run hatchery broodstock that returned as adults to freshwater in fall (fall run), spring-run offspring that returned in spring (spring run), and fall-run offspring that returned in spring (FRS). We found evidence for significant differentiation between the fall and federally listed threatened spring groups based on divergence at three circadian clock genes (OtsClock1b, OmyFbxw11, and Omy1009UW), but not neutral markers. We thus demonstrate the importance of genetic marker choice in resolving complex life history types. These findings directly impact conservation management strategies and add to previous evidence from Pacific and Atlantic salmon indicating that circadian clock genes influence migration timing.

O'Malley, Kathleen G; Jacobson, Dave P; Kurth, Ryon; Dill, Allen J; Banks, Michael A

2013-01-01

204

Genetic diversity within and among Pinus pinaster populations: comparison between AFLP and microsatellite markers.  

PubMed

Twenty-three populations of Pinus pinaster (13 Aquitaine populations and 10 Corsican populations) were analysed at three microsatellite loci and 122 AFLP loci. The aims of the study were: (i) to compare levels of within-population and among-population diversity assessed with both kinds of markers; (ii) to compare Aquitaine and Corsican provenances of P. pinaster; and (iii) to know if both markers gave the same information for conservation purposes. Classical population genetics statistics were estimated and the ranking of populations obtained using different markers and/or parameters were compared by computing Spearman's rank correlations. Even though microsatellites showed a higher within-population diversity, they showed the same level of differentiation as AFLP markers. Moreover, both markers also showed a higher genetic diversity in the Aquitaine provenance and a higher differentiation among Corsican populations. AFLPs and microsatellites gave different population diversity rankings. Consequently, the results do not support the potential population identification within each provenance for conservation purposes. PMID:11520347

Mariette, S; Chagné, D; Lézier, C; Pastuszka, P; Raffin, A; Plomion, C; Kremer, A

2001-04-01

205

Genetic evolutionary taboo search for optimal marker placement in infrared patient setup  

NASA Astrophysics Data System (ADS)

In infrared patient setup adequate selection of the external fiducial configuration is required for compensating inner target displacements (target registration error, TRE). Genetic algorithms (GA) and taboo search (TS) were applied in a newly designed approach to optimal marker placement: the genetic evolutionary taboo search (GETS) algorithm. In the GETS paradigm, multiple solutions are simultaneously tested in a stochastic evolutionary scheme, where taboo-based decision making and adaptive memory guide the optimization process. The GETS algorithm was tested on a group of ten prostate patients, to be compared to standard optimization and to randomly selected configurations. The changes in the optimal marker configuration, when TRE is minimized for OARs, were specifically examined. Optimal GETS configurations ensured a 26.5% mean decrease in the TRE value, versus 19.4% for conventional quasi-Newton optimization. Common features in GETS marker configurations were highlighted in the dataset of ten patients, even when multiple runs of the stochastic algorithm were performed. Including OARs in TRE minimization did not considerably affect the spatial distribution of GETS marker configurations. In conclusion, the GETS algorithm proved to be highly effective in solving the optimal marker placement problem. Further work is needed to embed site-specific deformation models in the optimization process.

Riboldi, M.; Baroni, G.; Spadea, M. F.; Tagaste, B.; Garibaldi, C.; Cambria, R.; Orecchia, R.; Pedotti, A.

2007-09-01

206

Genetic evolutionary taboo search for optimal marker placement in infrared patient setup.  

PubMed

In infrared patient setup adequate selection of the external fiducial configuration is required for compensating inner target displacements (target registration error, TRE). Genetic algorithms (GA) and taboo search (TS) were applied in a newly designed approach to optimal marker placement: the genetic evolutionary taboo search (GETS) algorithm. In the GETS paradigm, multiple solutions are simultaneously tested in a stochastic evolutionary scheme, where taboo-based decision making and adaptive memory guide the optimization process. The GETS algorithm was tested on a group of ten prostate patients, to be compared to standard optimization and to randomly selected configurations. The changes in the optimal marker configuration, when TRE is minimized for OARs, were specifically examined. Optimal GETS configurations ensured a 26.5% mean decrease in the TRE value, versus 19.4% for conventional quasi-Newton optimization. Common features in GETS marker configurations were highlighted in the dataset of ten patients, even when multiple runs of the stochastic algorithm were performed. Including OARs in TRE minimization did not considerably affect the spatial distribution of GETS marker configurations. In conclusion, the GETS algorithm proved to be highly effective in solving the optimal marker placement problem. Further work is needed to embed site-specific deformation models in the optimization process. PMID:17881802

Riboldi, M; Baroni, G; Spadea, M F; Tagaste, B; Garibaldi, C; Cambria, R; Orecchia, R; Pedotti, A

2007-10-01

207

Assessment of genetic diversity in Indian rice germplasm (Oryza sativa L.): use of random versus trait-linked microsatellite markers.  

PubMed

Assessment of genetic diversity in a crop germplasm is a vital part of plant breeding. DNA markers such as microsatellite or simple sequence repeat markers have been widely used to estimate the genetic diversity in rice. The present study was carried out to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic variability, and to assess the efficiency of random vis-á-vis QTL linked/gene based simple sequence repeat markers in diversity estimation. A set of 88 rice accessions that included landraces, farmer's varieties and popular Basmati lines were evaluated for agronomic traits and molecular diversity. The random set of SSR markers included 50 diversity panel markers developed under IRRI's Generation Challenge Programme (GCP) and the trait-linked/gene based markers comprised of 50 SSR markers reportedly linked to yield and related components. For agronomic traits, significant variability was observed, ranging between the maximum for grains/panicle and the minimum for panicle length. The molecular diversity based grouping indicated that varieties from a common centre were genetically similar, with few exceptions. The trait-linked markers gave an average genetic dissimilarity of 0.45 as against that of 0.37 by random markers, along with an average polymorphic information constant value of 0.48 and 0.41 respectively. The correlation between the kinship matrix generated by trait-linked markers and the phenotype based distance matrix (0.29) was higher than that of random markers (0.19). This establishes the robustness of trait-linked markers over random markers in estimating genetic diversity of rice germplasm. PMID:24371175

Yadav, Sheel; Singh, Ashutosh; Singh, M R; Goel, Nitika; Vinod, K K; Mohapatra, T; Singh, A K

2013-12-01

208

Analysis of genetic diversity in banana cultivars (Musa cvs.) from the South of Oman using AFLP markers and classification by phylogenetic, hierarchical clustering and principal component analyses*  

PubMed Central

Banana is an important crop grown in Oman and there is a dearth of information on its genetic diversity to assist in crop breeding and improvement programs. This study employed amplified fragment length polymorphism (AFLP) to investigate the genetic variation in local banana cultivars from the southern region of Oman. Using 12 primer combinations, a total of 1094 bands were scored, of which 1012 were polymorphic. Eighty-two unique markers were identified, which revealed the distinct separation of the seven cultivars. The results obtained show that AFLP can be used to differentiate the banana cultivars. Further classification by phylogenetic, hierarchical clustering and principal component analyses showed significant differences between the clusters found with molecular markers and those clusters created by previous studies using morphological analysis. Based on the analytical results, a consensus dendrogram of the banana cultivars is presented.

Opara, Umezuruike Linus; Jacobson, Dan; Al-Saady, Nadiya Abubakar

2010-01-01

209

Comparative analysis of genetic diversity in sacred lotus (Nelumbo nucifera Gaertn.) using AFLP and SSR markers.  

PubMed

The sacred lotus (Nelumbo nucifera Gaertn.) is an aquatic plant of economic and ornamental importance in China. In this study, we developed twenty novel sacred lotus SSR markers, and used AFLP and SSR markers to investigate the genetic diversity and genetic relationships among 58 accessions of N. nucifera including 15 seed lotus, 12 rhizome lotus, 24 flower lotus and 7 wild lotus. Our results showed that sacred lotus exhibited a low level of genetic diversity, which may attribute to asexual reproduction and long-term artificial selection. A dendrogram based on both AFLP and SSR clustering data showed that: (1) the seed lotus accessions and rhizome lotus accessions were distinctly clustered into different groups, which indicated the significant genetic differentiation between them. This may be attributed to the two modes of reproduction and lack of genetic exchange; (2) the accessions of Thailand wild lotus were separated from other wild lotus accessions. This implied that the Thailand lotus might be genetically differentiated from other wild lotuses. In addition, Mantel test conducted gave highly significant correlation between AFLP-SSR data and each of the AFLP and SSR ones, with the values of r = 0.941 and r = 0.879, respectively, indicating the higher efficiency of the combination of these techniques (AFLP and SSR) in estimation and validation of the genetic diversity among the accession of sacred lotus. This knowledge of the genetic diversity and genetic relatedness of N. nucifera is potentially useful to improve the current strategies in breeding and germplasm conservation to enhance the ornamental and economic value of sacred lotus. PMID:21735103

Hu, Jihong; Pan, Lei; Liu, Honggao; Wang, Shuzhen; Wu, Zhihua; Ke, Weidong; Ding, Yi

2012-04-01

210

Analysis of genetic diversity in Larix gmelinii (Pinaceae) with RAPD and ISSR markers.  

PubMed

Dahurian larch (Larix gmelinii), a deciduous conifer, is the northernmost tree, native to eastern Siberia and nearby regions of China. We used growth traits and molecular markers to assess genetic variation in different L. gmelinii growing regions; 105 individual samples were collected from seven regions of the Qingshan Forestry Centre, Heilongjiang Province, China. The greatest genetic regional variation was seen in the Youhao area, based on coefficients of variation for tree height, diameter and volume (14.73, 28.25, and 55.27%, respectively). Analysis using molecular markers showed rich genetic diversity. The RAPD and ISSR methods both indicated that most variation came from within populations. The seven regions were divided into two groups (Daxing'an and Xiaoxing'an Mountain ranges) by RAPD cluster analysis: Tianchi, Xiaojiuya, Yuanjiang, and Taiping regions were placed in the first group at a genetic distance of 0.08; while the other regions were in the second group. The correlation between RAPD markers and geographical distance was significant, with a correlation coefficient of 0.752. PMID:23408406

Zhang, L; Zhang, H G; Li, X F

2013-01-01

211

Association analysis, genetic diversity and structure analysis of tobacco based on AFLP markers.  

PubMed

Knowledge in the area of genetic diversity could aid in providing useful information in the selection of material for breeding such as hybridization programs and quantitative trait loci mapping. To this end, 50 Nicotiana tabacum genotypes were genotyped with 21 primer combination of amplified fragment length polymorphism (AFLP). A total of 480 unambiguous DNA fragments and 373 polymorphic bands were produced with an average of 17.76 per primer combination. Also, the results revealed high polymorphic rate varing from 52.63 to 92.59 %, demonstrating that AFLP technique utilized in this research can be a powerful and valuable tool in the breeding program of N. tabacum. Cluster analysis based on complete linkage method using Jaccard's genetic distance, grouped the 50 tobacco genotypes into eight clusters including three relatively big clusters, one cluster including Golden gift, Burly 7022 and Burly Kreuzung, one cluster consisting of two individuals (Pereg234, R9) and three single-member clusters (Pennbel69, Coker176 and Budisher Burley E), Recent genotypes showed high genetic distance from other genotypes belonging to cluster I and II. Association analysis between seven important traits and AFLP markers were performed using four statistical models. The results revealed the model containing both the factors, population structure (Q) and general similarity in genetic background arising from shared kinship (K), reduces false positive associations between markers and phenotype. According to the results nine markers were determined that could be considered to be the most interesting candidates for further studies. PMID:24488320

Dadras, Ahmad Reza; Sabouri, Hossein; Nejad, Ghasem Mohammadi; Sabouri, Atefeh; Shoai-Deylami, Mardavij

2014-05-01

212

Genetic epidemiology of osteoporosis across four microsatellite markers near the VDR gene  

PubMed Central

The large amount of positive genetic association data in a number of bone diseases suggests functional consequences of Vitamin D receptor (VDR) gene polymorphism. In the present study, four microsatellite markers viz., D12S1633, D12S1635, D12S347, and D12S96, that lie in the vicinity of the VDR gene on chromosome 12 were selected to assess the allele distribution pattern and diversity among three groups of individuals - normal, osteopenia and osteoporosis. Genetic association study was performed using allele frequency data. Total genomic DNA was isolated from the whole blood of 226 individuals, after recording their bone mineral density (BMD) using Dual X-ray absorptiometry (DXA). All DNA samples were subjected to multiplex Polymerase Chain Reaction (PCR) - genotyping. Allele frequencies and genetic diversity parameters like - number of alleles, average variance and average heterozygosity across all the four markers among three groups were computed. Effect of population stratification was excluded by investigating population structure. A trend of decreasing genetic diversity across four loci from normal to pre- and post-disease condition has been observed. Lesser recombination rate (?) indicates linkage between studied microsatellite markers and VDR gene. Statistically significant linkage disequilibrium was detected for the allele - 22 of locus D12S96 with osteoporosis. A positive association of allele - 22 suggests susceptibility to disease whereas predominance of allele - 27 among non - diseased group implicates its association with normal bone health.

Raje, Mehrunnisa; Botre, Chaitali; Ashma, Richa

2013-01-01

213

Patterns of genetic architecture for life-history traits and molecular markers in a subdivided species.  

PubMed

Understanding the utility and limitations of molecular markers for predicting the evolutionary potential of natural populations is important for both evolutionary and conservation genetics. To address this issue, the distribution of genetic variation for quantitative traits and molecular markers is estimated within and among 14 permanent lake populations of Daphnia pulicaria representing two regional groups from Oregon. Estimates of population subdivision for molecular and quantitative traits are concordant, with QST generally exceeding GST. There is no evidence that microsatellites loci are less informative about subdivision for quantitative traits than are allozyme loci. Character-specific comparison of QST and GST support divergent selection pressures among populations for the majority of life-history traits in both coast and mountain regions. The level of within-population variation for molecular markers is uninformative as to the genetic variation maintained for quantitative traits. In D. pulicaria, regional differences in the frequency of sex may contribute to variation in the maintenance of expressed within-population quantitative-genetic variation without substantially impacting diversity at the genic level. These data are compared to an identical dataset for 17 populations of the temporary-pond species, D. pulex. PMID:11681731

Morgan, K K; Hicks, J; Spitze, K; Latta, L; Pfrender, M E; Weaver, C S; Ottone, M; Lynch, M

2001-09-01

214

Physical mapping of genetic markers on the short arm of chromosome 5  

SciTech Connect

The deletion of the short arm of chromosome 5 is associated with the cri-du-chat syndrome. In addition, loss of this portion of a chromosome is a common cytogenetic marker in a number of malignancies. However, to date, no genes associated with these disorders have been identified. Physical maps are the first step in isolating causative genes, and genes involved in autosomal recessive disorders are now routinely mapped through the identification of linked markers. Extensive genetic maps based upon polymorphic short tandem repeats (STRs) have provided researchers with a large number of markers to which such disorders can be genetically mapped. However, the physical locations of many of these STRs have not been determined. Toward the goal of integrating the human genetic maps with the physical maps, a 5p somatic cell hybrid deletion mapping panel that was derived from patients with 5p deletions or translocations was used to physically map 47 STRs that have been used to construct genetic maps of 5p. These data will be useful in the localization of disease genes that map to 5p and may be involved in the etiology of the cri-du-chat syndrome. 26 refs., 1 fig.

Gersh, M.; Goodart, S.A.; Overhauser, J. [Thomas Jefferson Univ., Philadelphia, PA (United States)] [Thomas Jefferson Univ., Philadelphia, PA (United States)

1994-12-01

215

Contrasting genetic structures of two parasitic nematodes, determined on the basis of neutral microsatellite markers and selected anthelmintic resistance markers.  

PubMed

For the first time, the neutral genetic relatedness of natural populations of Trichostrongylid nematodes was investigated in relation to polymorphism of the beta-tubulin gene, which is selected for anthelminthic treatments. The aim of the study was to assess the contribution of several evolutionary processes: migration and genetic drift by neutral genetic markers and selection by anthelminthic treatments on the presence of resistance alleles at beta-tubulin. We studied two nematode species (Teladorsagia circumcincta and Haemonchus contortus) common in temperate climatic zones; these species are characterized by contrasting life history traits. We studied 10 isolated populations of goat nematode parasites: no infected adult goat had been exchanged after the herds were established. Beta-tubulin polymorphism was similar in these two species. One and two beta-tubulin alleles from T. circumcincta and H. contortus respectively were shared by several populations. Most of the beta-tubulin alleles were 'private' alleles. No recombination between alleles was detected in BZ-resistant alleles from T. circumcincta and H. contortus. The T. circumcincta populations have not diverged much since their isolation (F(ST) <0.08), whereas H. contortus displayed marked local genetic differentiation (F(ST) ranging from 0.08 to 0.18). These findings suggest that there are severe bottlenecks in the H. contortus populations, possibly because of their reduced abundance during unfavourable periods and their high reproductive rate, which allows the species to persist even after severe population reduction. Overall, the data reported contradict the hypothesis of the origin of beta-tubulin resistance alleles in these populations from a single mutational event, but two other hypotheses (recurrent mutation generating new alleles in isolated populations and the introduction of existing alleles) emerge as equally likely. PMID:19900171

Silvestre, A; Sauve, C; Cortet, J; Cabaret, J

2009-12-01

216

Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago sativa) using microsatellite and AFLP markers  

Microsoft Academic Search

BACKGROUND: Alfalfa (Medicago sativa) is a major forage crop. The genetic progress is slow in this legume species because of its autotetraploidy and allogamy. The genetic structure of this species makes the construction of genetic maps difficult. To reach this objective, and to be able to detect QTLs in segregating populations, we used the available codominant microsatellite markers (SSRs), most

Bernadette Julier; Sandrine Flajoulot; Philippe Barre; Gaëlle Cardinet; Sylvain Santoni; Thierry Huguet; Christian Huyghe

2003-01-01

217

Genetic divergence of rubber tree estimated by multivariate techniques and microsatellite markers  

PubMed Central

Genetic diversity of 60 Hevea genotypes, consisting of Asiatic, Amazonian, African and IAC clones, and pertaining to the genetic breeding program of the Agronomic Institute (IAC), Brazil, was estimated. Analyses were based on phenotypic multivariate parameters and microsatellites. Five agronomic descriptors were employed in multivariate procedures, such as Standard Euclidian Distance, Tocher clustering and principal component analysis. Genetic variability among the genotypes was estimated with 68 selected polymorphic SSRs, by way of Modified Rogers Genetic Distance and UPGMA clustering. Structure software in a Bayesian approach was used in discriminating among groups. Genetic diversity was estimated through Nei's statistics. The genotypes were clustered into 12 groups according to the Tocher method, while the molecular analysis identified six groups. In the phenotypic and microsatellite analyses, the Amazonian and IAC genotypes were distributed in several groups, whereas the Asiatic were in only a few. Observed heterozygosity ranged from 0.05 to 0.96. Both high total diversity (HT' = 0.58) and high gene differentiation (G st' = 0.61) were observed, and indicated high genetic variation among the 60 genotypes, which may be useful for breeding programs. The analyzed agronomic parameters and SSRs markers were effective in assessing genetic diversity among Hevea genotypes, besides proving to be useful for characterizing genetic variability.

2010-01-01

218

Mapping and analysis of quantitative trait loci in Lycopersicon (tomato) with the aid of genetic markers using approximate maximum likelihood methods  

Microsoft Academic Search

1691 F-2 progeny of a cross between Lycopersicon esculentum and L pimpinellifolium grown under field conditions were scored for 18 quantitative traits of economic interest and 10 segregating genetic markers. Each parental strain was homozygous for one allele of each marker. Four of the markers were electrophoretic, and six were morphological. Three pairs of the genetic markers were linked. An

J I Weller

1987-01-01

219

Analysis of genetic diversity among wild bermudagrass germplasm from southwest China using SSR markers.  

PubMed

Fifty-five wild accessions of bermudagrass (Cynodon dactylon) were collected from southwest China (Sichuan, Chongqing, Yunnan, Guizhou, and Tibet), and their genetic diversity was analyzed using simple sequence repeat markers. A total of 267 polymorphic bands were detected with 18 primer combinations. The genetic similarity among the accessions ranged from 0.688 to 0.894 with an average of 0.797. All 55 wild accessions were clustered into 7 eco-geographic groups. Our data showed that the dendrogram was almost in accordance with geographic distribution, and accessions from the same collection sites tended to be clustered into the same group. A genetic differentiation analysis revealed that the percentage of genetic variance was 70.07 and 29.93% within and among groups, respectively. Finally, we discuss the implications of these results for C. dactylon in southwest China. PMID:23096923

Ling, Y; Zhang, X-Q; Ma, X; Chen, S-Y; Chen, T-T; Liu, W

2012-01-01

220

Genetic diversity and population differentiation in the cockle Cerastoderma edule estimated by microsatellite markers  

NASA Astrophysics Data System (ADS)

The edible cockle Cerastoderma edule is a marine bivalve commercially fished in several European countries that have lately suffered a significant decrease in production. Despite its commercial importance, genetic studies in this species are scarce. In this work, genetic diversity and population differentiation of C. edule has been assessed using 11 microsatellite markers in eight locations from the European Atlantic coast. All localities showed similar observed and expected heterozygosity values, but displayed differences in allelic richness, with lowest values obtained for localities situated farther north. Global Fst value revealed the existence of significant genetic structure; all but one locality from the Iberian Peninsula were genetically homogeneous, while more remote localities from France, The Netherlands, and Scotland were significantly different from all other localities. A combined effect of isolation by distance and the existence of barriers that limit gene flow may explain the differentiation observed.

Martínez, L.; Méndez, J.; Insua, A.; Arias-Pérez, A.; Freire, R.

2013-03-01

221

Development of microsatellite markers from an enriched genomic library for genetic analysis of melon (Cucumis melo L.)  

PubMed Central

Background Despite the great advances in genomic technology observed in several crop species, the availability of molecular tools such as microsatellite markers has been limited in melon (Cucumis melo L.) and cucurbit species. The development of microsatellite markers will have a major impact on genetic analysis and breeding of melon, especially on the generation of marker saturated genetic maps and implementation of marker assisted breeding programs. Genomic microsatellite enriched libraries can be an efficient alternative for marker development in such species. Results Seven hundred clones containing microsatellite sequences from a Tsp-AG/TC microsatellite enriched library were identified and one-hundred and forty-four primer pairs designed and synthesized. When 67 microsatellite markers were tested on a panel of melon and other cucurbit accessions, 65 revealed DNA polymorphisms among the melon accessions. For some cucurbit species, such as Cucumis sativus, up to 50% of the melon microsatellite markers could be readily used for DNA polymophism assessment, representing a significant reduction of marker development costs. A random sample of 25 microsatellite markers was extracted from the new microsatellite marker set and characterized on 40 accessions of melon, generating an allelic frequency database for the species. The average expected heterozygosity was 0.52, varying from 0.45 to 0.70, indicating that a small set of selected markers should be sufficient to solve questions regarding genotype identity and variety protection. Genetic distances based on microsatellite polymorphism were congruent with data obtained from RAPD marker analysis. Mapping analysis was initiated with 55 newly developed markers and most primers showed segregation according to Mendelian expectations. Linkage analysis detected linkage between 56% of the markers, distributed in nine linkage groups. Conclusions Genomic library microsatellite enrichment is an efficient procedure for marker development in melon. One-hundred and forty-four new markers were developed from Tsp-AG/TC genomic library. This is the first reported attempt of successfully using enriched library for microsatellite marker development in the species. A sample of the microsatellite markers tested proved efficient for genetic analysis of melon, including genetic distance estimates and identity tests. Linkage analysis indicated that the markers developed are dispersed throughout the genome and should be very useful for genetic analysis of melon.

Ritschel, Patricia Silva; Lins, Tulio Cesar de Lima; Tristan, Rodrigo Lourenco; Buso, Glaucia Salles Cortopassi; Buso, Jose Amauri; Ferreira, Marcio Elias

2004-01-01

222

Analysis of eight polymorphic human genetic markers in a well-defined Greek population.  

PubMed

The use of DNA in forensic science has become a basic tool for person identification or parentage testing. The use of polymorphic markers permits the formation of a unique profile for each individual. The knowledge of allele frequencies in a given population allows the scientist to estimate the probability of a particular allele combination. For this task, allele databanks are essential. In this report, the authors estimate the frequencies of eight polymorphic markers (namely, HumFES, HumF13A1, HumTHO1, HumVWA, HumFABP2, HumLIPOL, D1S80, and D17S5) in a randomly selected sample from Crete, Greece. The allele profile of all markers, with the exception of D17S5 and HumFABP2, concurs with previous reports and international data. PMID:10871135

Tsopanomichalou, M; Sourvinos, G; Arvanitis, D; Michalodimitrakis, M

2000-06-01

223

Using Genetic Markers to Identify Lung Cancer in Fine Needle Aspiration Samples  

PubMed Central

Purpose We seek to establish a genetic test to identify lung cancer using cells obtained through CT guided fine needle aspiration (FNA). Experimental Design We selected regions of frequent copy number gains in chromosomes 1q32, 3q26, 5p15, and 8q24 in non-small cell lung cancer (NSCLC) and tested their ability to determine the neoplastic state of cells obtained by FNA using fluorescent in situ hybridization (FISH). Two sets of samples were included. The pilot set included six paraffin-embedded non-cancerous lung tissues and 33 formalin-fixed FNA specimens. These 39 samples were used to establish the optimal fixation and single scoring criteria for the samples. The test set included 40 FNA samples. The results of the genetic test were compared with the cytology, pathology, and clinical follow up for each case to assess the sensitivity and specificity of the genetic test. Results Non-tumor lung tissues had ?4 signals per nuclei for all tested markers while tumor samples had ?5 signals per nucleus in five or more cells for at least one marker. Among the 40 testing cases, 36 of 40 (90%) FNA samples were analyzable. Genetic analysis identified 15 cases as tumor and 21 as non-tumor. Clinical and pathological diagnoses confirmed the genetic test in 15 of 16 lung cancer cases regardless of tumor subtype, stage, or size and in 20 of 20 cases diagnosed as benign lung diseases. Conclusions A set of only four genetic markers can distinguish the neoplastic state of lung lesion using small samples obtained through CT guided FNA.

Gill, Rajbir K.; Vazquez, Madeline F.; Kramer, Arin; Hames, Megan; Zhang, Lijuan; Heselmeyer-Haddad, Kerstin; Ried, Thomas; Shilo, Konstantin; Henschke, Claudia; Yankelevitz, David; Jen, Jin

2008-01-01

224

Genetic variability of six indigenous goat breeds using major histocompatibility complex-associated microsatellite markers  

PubMed Central

The present study aimed at analyzing the genetic variability of indigenous goat breeds (Capra hircus) using the MHC-associated microsatellite markers BF1, BM1818, BM1258, DYMS1, and SMHCC1. The following breeds were included: Chinese Xuhuai, Indian Changthangi and Pashmina, Kenyan Small East African (SEA) and Galla, and Albanian Vendi. To examine genetic variability, the levels of heterozigosity, degrees of inbreeding, and genetic differences among the breeds were analyzed. The mean number of alleles ranged from nine in the Galla to 14.5 in the Vendi breed. The mean observed heterozygosity and mean expected heterozygosity varied from 0.483 in the Vendi to 0.577 in the Galla breed, and from 0.767 in the SEA to 0.879 in the Vendi breed, respectively. Significant loss of heterozygosity (p < 0.01) indicated that these loci were not in Hardy-Weinberg equilibrium. The mean FIS values ranged from 0.3299 in the SEA to 0.4605 in the Vendi breed with a mean value of 0.3623 in all breeds (p < 0.001). Analysis of molecular variance indicated that 7.14% and 4.74% genetic variation existed among the different breeds and geographic groups, whereas 92.86% and 95.26% existed in the breeds and the geographic groups, respectively (p < 0.001). The microsatellite marker analysis disclosed a high degree of genetic polymorphism. Loss of heterozygosity could be due to genetic drift and endogamy. The genetic variation among populations and geographic groups does not indicate a correlation of genetic differences with geographic distance.

de Andrade Salles, Patricy; Santos, Silvana C.; Rondina, Davide

2011-01-01

225

Microsatellite loci in the carcinogenic liver fluke, Opisthorchis viverrini and their application as population genetic markers.  

PubMed

Opisthorchis viverrini is a carcinogenic foodborne trematode endemic in Southeast Asia especially in Thailand and the Lao People's Democratic Republic. Opisthorchiasis causes hepatobiliary diseases and cholangiocarcinoma (bile duct cancer). Currently there is substantial evidence on genetic variation of O. viverrini but the information on population genetic structure is lacking. Because microsatellite DNA of this parasite is not available, we for the first time isolated and utilized microsatellite DNA as genetic markers to examine genetic diversity and the population structure of O. viverrini. Partial genomic DNA libraries were constructed by conventional and enrichment methods which yielded microsatellite-containing clones of 0.18-0.25% and 16.84%, respectively. Within 41 microsatellite loci isolated 36.59% were perfect, 60.98% were interrupted and 2.44% were compound microsatellites. The CA repetitions were the most frequent, followed by GT and CAT. Primers specific to the flanking regions of 12 microsatellite loci were developed to genotype 150 O. viverrini individuals from geographical localities in Thailand and Lao PDR. Allele numbers per locus ranged from 2 to 15, with the mean expected heterozygosity of 0.03-0.66. Analyses of O. viverrini from 5 localities revealed a high level of genetic diversity and had significant deviation from Hardy-Weinberg equilibrium. Significant heterozygote deficiency as well as heterozygote excess was detected across all localities indicating the possibility of selfing (inbreeding) as a predominant reproductive mode. Significant genetic differentiation (F(ST)) was also detected between worms from different localities with varying levels of genetic heterogeneity. We discuss our results in terms of what these novel microsatellite markers reveal about the epidemiology and transmission dynamics of this medically important parasite, both in terms of the current study and their potential for future comprehensive population genetic studies O. viverrini sensu lato in Southeast Asia. PMID:19900579

Laoprom, Nonglak; Sithithaworn, Paiboon; Ando, Katsuhiko; Sithithaworn, Jiraporn; Wongkham, Sopit; Laha, Thewarach; Klinbunga, Sirawut; Webster, Joanne P; Andrews, Ross H

2010-01-01

226

Use of the IRAP marker to study genetic variability in Pseudocercospora fijiensis populations.  

PubMed

Pseudocercospora fijiensis is the etiological agent of black Sigatoka, which is currently considered as one of the most destructive banana diseases in all locations where it occurs. It is estimated that a large portion of the P. fijiensis genome consists of transposable elements, which allows researchers to use transposon-based molecular markers in the analysis of genetic variability in populations of this pathogen. In this context, the inter-retrotransposon-amplified polymorphism (IRAP) was used to study the genetic variability in P. fijiensis populations from different hosts and different geographical origins in Brazil. A total of 22 loci were amplified and 77.3 % showed a polymorphism. Cluster analysis revealed two major groups in Brazil. The observed genetic diversity (H E) was 0.22, and through molecular analysis of variance, it was determined that the greatest genetic variability occurs within populations. The discriminant analysis of principal components revealed no structuring related to the geographical origin of culture of the host. The IRAP-based marker system is a suitable tool for the study of genetic variability in P. fijiensis. PMID:24190756

de Queiroz, Casley Borges; Santana, Mateus Ferreira; da Silva, Gilvan Ferreira; Mizubuti, Eduardo Seiti Gomide; de Araújo, Elza Fernandes; de Queiroz, Marisa Vieira

2014-03-01

227

Genetic diversity of two haploid markers in the Udegey population from southeastern Siberia.  

PubMed

The Udegeys are a small ethnic group who live along the tributaries of the Amur River Basin of southeastern Siberia in Russia. They are thought to speak a language belonging to a subdivision of the Tungusic-Manchu branch of the Altaic family. To understand the genetic features and genetic history of the Udegeys, we analyzed two haploid markers, mitochondrial DNA (mtDNA), and Y-chromosomal variation, in 51 individuals (including 21 males) from the Udegey population. In general, the Udegeys' mtDNA profiles revealed similarities to Siberians and other northeastern Asian populations, although a moderate European contribution was also detected. Interestingly, pairwise values of F(ST) and the MDS plots based on the mtDNA variation showed that the Orok and Nivkh inhabiting the very same region of the Udegey were significantly different from the Udegey, implying that they may have been isolated and undergone substantial genetic drift. The Udegeys were characterized by a high frequency (66.7%) of Y chromosome haplogroup C, indicating a close genetic relationship with Mongolians and Siberians. On the paternal side, however, very little admixture was observed between the Udegeys and Europeans. Thus, the combined haploid genetic markers of both mtDNA and the Y chromosome imply that the Udegeys are overall closest to Siberians and northeast Asians of the Altaic linguistic family, with a minor maternal contribution from the European part of the continent. PMID:19953529

Jin, Han-Jun; Kim, Ki-Cheol; Kim, Wook

2010-06-01

228

PERMANENT GENETIC RESOURCES: Characterization of microsatellite markers for the almendro (Dipteryx panamensis), a tetraploid rainforest tree.  

PubMed

The almendro (Dipteryx panamensis, Fabaceae) is a tetraploid tree native to the Atlantic lowland rainforests of Central America. We present nine microsatellite primer pairs amplified in three multiplexed reactions for 549 individuals from four sites in Costa Rica. All loci were polymorphic, ranging from three to 13 alleles per locus. Expected heterozygosity was estimated with the program tetrasat, and ranged from 0.21 to 0.74 across loci. These markers will be used for estimating pollen dispersal, seed dispersal, genetic structure and genetic diversity in fragmented landscapes. PMID:21585810

Hanson, Thor R; Brunsfeld, Steven J; Finegan, Bryan; Waits, Lisette P

2008-03-01

229

Genetic diversity in Tunisian Crataegus azarolus L. var. aronia L. populations assessed using RAPD markers  

Microsoft Academic Search

– \\u000a \\u000a • The genetic diversity of nine wild Tunisian Crataegus azarolus var. aronia L. populations from different bioclimates was assessed using RAPD markers.\\u000a \\u000a \\u000a \\u000a \\u000a – \\u000a \\u000a • Eight selected primers generated a total of 105 bands, 81 of which were polymorphic. Shannon’s index (H?) ranged from 0.222 to 0.278 according to a population with an average of 0.245. The genetic variation within

Chayma Rajeb; Chokri Messaoud; Hnia Chograni; Afef Bejaoui; Abdennacer Boulila; Mohamed Nejib Rejeb; Mohamed Boussaid

2010-01-01

230

A genetic marker in the variable region of rabbit immunoglobulin heavy chain.  

PubMed Central

A previous study [Mole et al. (1971) Biochem. J. 124, 301-318] showed several differences in sequence between the variable (V) regions of rabbit immunoglobulin Aa1 and Aa3 heavy chains. The inheritance of one such difference has been followed in a family of 38 rabbits by a radioautographic peptide-'map' technique and is shown to segregate in a Mendelian fashion. This clearly demonstrates the presence of a genetic marker in the rabbit heavy-chain V region, although the finding that Aa2 and Aa3 heavy chains have identity of sequence in the region studied obscures the relationship of this genetic marker to the a locus. Images PLATE 1 PLATE 2 PLATE 3 PLATE 4 PLATE 5

Mole, L R

1975-01-01

231

Genetic similarity among Tunisian olive cultivars and two unknown feral olive trees estimated through SSR markers.  

PubMed

We used eight informative microsatellite markers for fingerprinting and evaluation of genetic similarity among 15 Tunisian olive (Olea europaea L.) cultivars and two feral unknown trees named Soulela 1 and Soulela 2. Thirty-one alleles were revealed, and the number of alleles per SSR varied from 2 (UDO12) to 6 (GAPU71A). Cluster analysis grouped cultivars into three main clusters. The two unknown varieties could not be reliably classified into any of these cultivar groups. SSR analysis indicated the presence of three erroneous denominations of cultivars. We resolved two synonymy cases (Zalmati and Chemlali; Rkhami and Chetoui) and one case of homonymy (Chemlali Tataouine). Genetic analyses of DNA extracted from leaves, oils, and embryos of the two unknown cultivars and the two major Tunisian olive cultivars (Chemlali and Chetoui) were also studied. We conclude that the reliable identification of these two feral cultivars needs to be addressed by a larger set of markers. PMID:24535154

Ben-Ayed, Rayda; Sans-Grout, Cinderella; Moreau, Fabienne; Grati-Kamoun, Naziha; Rebai, Ahmed

2014-06-01

232

Genetic hetergoeneity in X-linked hydrocephalus: Linkage to markers within Xq27. 3  

SciTech Connect

X-linked hydrocephalus is a well-defined disorder which accounts for [ge]70% of hydrocephalus in males. Pathologically, the conditions is characterized by stenosis or obliteration of the aqueduct of Sylvius. Previous genetic linkage studies have suggested likelihood of genetic homogeneity for this condition, with close linkage to the DXS52 and F8C markers in Xq28. The authors have investigated a family with typical X-linked aqueductal stenosis, in which no linkage to these markers was present. In this family, close linkage was established to the DXS548 and FRAXA loci in Xq27.3. The findings demonstrate that X-linked aqueductal stenosis may result from mutations at two different loci on the X chromosome. Caution is indicated in using linkage for the prenatal diagnosis of X-linked hydrocephalus. 43 refs., 2 figs., 2 tabs.

Strain, L.; Brock, D.J.H.; Bonthron, D.T. (Univ. of Edinburgh (United Kingdom)); Gosden, C.M. (Western General Hospital, Edinburgh (United Kingdom))

1994-02-01

233

Genetic linkage map of human chromosome 7 with 63 DNA markers.  

PubMed Central

High-density genetic maps of individual human chromosomes will permit accurate localization of disease-associated genes and provide signposts that will be useful in the construction of physical maps. We have constructed a genetic map of chromosome 7 with 63 polymorphic DNA markers by using segregation data from 23 three-generation families and recently developed multilocus linkage-analysis techniques. The map spans 250 centimorgans in females and 170 centimorgans in males, with much of the difference being concentrated in a few intervals. The density and informativeness of the markers are such that there is a high probability of detecting linkage to any disease gene on this chromosome for which 20 phase-known meioses are available. Images

Barker, D; Green, P; Knowlton, R; Schumm, J; Lander, E; Oliphant, A; Willard, H; Akots, G; Brown, V; Gravius, T

1987-01-01

234

Genetic relationships among seven sections of genus Arachis studied by using SSR markers  

PubMed Central

Background The genus Arachis, originated in South America, is divided into nine taxonomical sections comprising of 80 species. Most of the Arachis species are diploids (2n = 2x = 20) and the tetraploid species (2n = 2x = 40) are found in sections Arachis, Extranervosae and Rhizomatosae. Diploid species have great potential to be used as resistance sources for agronomic traits like pests and diseases, drought related traits and different life cycle spans. Understanding of genetic relationships among wild species and between wild and cultivated species will be useful for enhanced utilization of wild species in improving cultivated germplasm. The present study was undertaken to evaluate genetic relationships among species (96 accessions) belonging to seven sections of Arachis by using simple sequence repeat (SSR) markers developed from Arachis hypogaea genomic library and gene sequences from related genera of Arachis. Results The average transferability rate of 101 SSR markers tested to section Arachis and six other sections was 81% and 59% respectively. Five markers (IPAHM 164, IPAHM 165, IPAHM 407a, IPAHM 409, and IPAHM 659) showed 100% transferability. Cluster analysis of allelic data from a subset of 32 SSR markers on 85 wild and 11 cultivated accessions grouped accessions according to their genome composition, sections and species to which they belong. A total of 109 species specific alleles were detected in different wild species, Arachis pusilla exhibited largest number of species specific alleles (15). Based on genetic distance analysis, the A-genome accession ICG 8200 (A. duranensis) and the B-genome accession ICG 8206 (A. ipaënsis) were found most closely related to A. hypogaea. Conclusion A set of cross species and cross section transferable SSR markers has been identified that will be useful for genetic studies of wild species of Arachis, including comparative genome mapping, germplasm analysis, population genetic structure and phylogenetic inferences among species. The present study provides strong support based on both genomic and genic markers, probably for the first time, on relationships of A. monticola and A. hypogaea as well as on the most probable donor of A and B-genomes of cultivated groundnut.

2010-01-01

235

Organophosphorus hydrolase: a multifaceted plant genetic marker which is selectable, scorable, and quantifiable in whole seed.  

PubMed

Organophosphorus hydrolase (OPH, EC 3.1.8.1) provides a novel function as an alternative genetic marker system for use in many types of plant transformations. OPH is a high-capacity hydrolase with multiple organophosphorus substrates, many of which are neurotoxins and thus used extensively as pesticides. This spectrum of organophosphates includes compounds that are phytotoxic as well as those that are hydrolyzed to products that are easily detected visually without significant disruption of plant health. This dichotomy gives OPH the features of both a selectable marker as well as that of a scorable marker system, and these characteristics have been tested at several stages during the plant transformation and regeneration process. Finally, it is possible to quantify hydrolytic activity in the seed without interfering with its subsequent growth and regeneration. PMID:22350995

Pinkerton, T Scott; Wild, James R; Howard, John A

2012-01-01

236

Genetic analysis of apomixis in Citrus and Poncirus by molecular markers  

Microsoft Academic Search

Propagation of citrus rootstocks depends upon the production of clonal plants from nucellar seedlings. This makes apomixis\\u000a one of the host important traits in breeding programs for citrus rootstocks. The genetic control of apomixis was studied in\\u000a a 50-tree progeny derived from the cross C. volkameriana?P. trifoliata using 69 molecular markers and bulked segregant analysis. The proportion of nucellar seedlings

R. García; M. J. Asíns; J. Forner; E. A. Carbonell

1999-01-01

237

UNC study finds genetic marker in vitamin D receptor gene associated with increased pancreatic cancer survival  

Cancer.gov

Pancreatic cancer patients with a genetic marker linked to increased expression of the receptor for vitamin D have higher rates of overall survival, according to findings presented at the American Association for Cancer Research's Pancreatic Cancer: Progress and Challenges conference, held in Lake Tahoe, Nev., June 18-21. The study was conducted by scientists from the University of North Carolina at Chapel Hill Eshelman School of Pharmacy. UNC is home to the Lineberger Comprehensive Cancer Center.

238

Comparison off genetic distance and order off DNA markers in five populations of rice.  

PubMed

A group of about 300 evenly distributed DNA markers from a high density RFLP linkage map of rice constructed using an F2 population derived from a japonica variety, Nipponbare, and an indica variety, Kasalath, were used to evaluate gene order and genetic distance in four other rice mapping populations. The purpose of this study was to determine the degree to which information gained from the high density linkage map could be applied to other mapping populations, particularly with regard to its utility in bridging quantitative traits and molecular and physical mapping information. The mapping populations consisted of two F2 populations derived from Dao Ren Qiao/Fl-1084 and Kinandangputi/Fl-1007, recombinant inbred lines from Asominori/IR24, and a backcross population from Sasanishiki/Habataki//Sasanishiki. All DNA markers commonly mapped in the four populations showed the same linkage groups as in the Nipponbare/Kasalath linkage map with conserved linkage order. The genetic distance between markers among the different populations did not vary to a significant level in any of the 12 chromosomes. The differences in some markers could be attributed to the size of the population used in the construction of the linkage maps. Furthermore, the conservation of linkage order found in the distal region of chromosomes 11 and 12 was also confirmed in the RFLP maps based on the four populations of rice. These suggest that any major genetic information from the Nipponbare/Kasalath map can be expected to be approximately the same in other crosses or populations. This high density RFLP linkage map, which is being utilized in constructing a physical map of rice, can be very useful in interpreting genome structure with great accuracy in other populations. Key words : linkage map, japonica, indica, gene order, genetic distance. PMID:18469946

Antonio, B A; Inoue, T; Kajiya, H; Nagamura, Y; Kurata, N; Minobe, Y; Yano, M; Nakagahra, M; Sasaki, T

1996-10-01

239

Molecular Marker Studies in Riverine Buffaloes, for Characterization and Diagnosis of Genetic Defects  

Microsoft Academic Search

The buffalo is probably the last livestock species to have been domesticated, with many genetic, physiological and behavioural\\u000a traits not yet well understood. Molecular markers have been used for characterizing animals and breeds, diagnosing diseases\\u000a and identifying anatomical and physiological anomalies. RFLP studies showed low heterozygosity, but genomic and oligonucleotide\\u000a probes showed species-specific bands useful for identification of carcass or

B. R. Yadav

240

A genetic map of melon (Cucumis melo L.) based on amplified fragment length polymorphism (AFLP) markers  

Microsoft Academic Search

Genetic maps facilitate the study of genome structure and evolution, and the identification of monogenic traits or Mendelian\\u000a components of quantitative traits. We evaluated 228 RAPD, microsatellite and AFLP markers for linkage analysis in melon (Cucumis melo L.) varieties MR-1 (resistant to Fusarium wilt, powdery and downy mildews) and Ananas Yokneum (AY; susceptible to these diseases) and constructed a detailed

Y.-H. Wang; C. E. Thomas; R. A. Dean

1997-01-01

241

[Cloning goat producing human lactoferrin with genetically modified donor cells selected by single or dual markers].  

PubMed

We compared the efficiency of cloning goat using human lactoferrin (hLF) with genetically modified donor cells marked by single (Neo(r)) or double (Neo(r)/GFP) markers. Single marker expression vector (pBLC14) or dual markers expression vector (pAPLM) was delivered to goat fetal fibroblasts (GFF), and then the transgenic GFF was used as donor cells to produce transgenic goats. Respectively, 58.8% (20/34) and 86.7% (26/30) resistant cell lines confirmed the transgenic integration by PCR. Moreover, pAPLM cells lines were subcultured with several passages, only 20% (6/30) cell lines was observed fluorescence from each cell during the cell passage. Somatic cell nuclear transfer using the donor cells harbouring pBLC14 or pAPLM construct, resulting in a total of 806 reconstructed embryos, a pregnancy rate at 35 d (53.8%, 39.1%) and 60 d (26.9%, 21.7%), and an offspring birth rate (1.9%, 1.4%) with 5 and 7 newborn cloned goats, respectively. Transgene was confirmed by PCR and southern-blot in all cloned offspring. There were no significant differences at the reconstructed embryo fusion rates, pregnancy rates and the birth rate (P > 0.05) between single and double markers groups. The Neo(r)/GFP double markers could improve the reliability for accurately and efficiently selecting the genetically modified donor cells. No adverse effect was observed on the efficiency of transgenic goat production by SCNT using somatic cells transfected with double (Neo(r)/GFP) markers vector. PMID:23593872

An, Liyou; Yuan, Yuguo; Yu, Baoli; Yang, Tingjia; Cheng, Yong

2012-12-01

242

Genetic diversity of maize germplasm assessed by retrotransposon-based markers.  

PubMed

Maize is one of the most important crops and also a model for grass genome research. Transposable elements comprise over 78% of the maize genome and their ability to generate new copies makes them good potential markers. Interretrotransposon-amplified polymorphism (IRAP) and retrotransposon microsatellite amplified polymorphism (REMAP) protocols were used for the first time in maize to study the genetic variability between maize cultivars. Ten PCR primers were selected based on a systematic analysis of the sequence conservation in the extremities of different high copy number transposable elements, whereas one primer was chosen based on a microsatellite sequence. Of the 16 primer combinations tested, 14 produced polymorphic bands. These markers were used to identify genetic similarity among 20 maize cultivars selected by their different kernel oil content. Genetic similarity analysis was performed based on the polymorphic band profiles and dendrograms were developed by the unweighted pair-group method with arithmetic averages. Clustering technique revealed that samples were grouped into three clusters that differed in their kernel oil content and size, and in their relative embryo size. In the current investigation, there is evidence that IRAP/REMAP may be useful as markers in maize. PMID:24634146

Kuhn, Betty Cristiane; López-Ribera, Ignacio; da Silva Machado, Maria de Fátima Pires; Vicient, Carlos M

2014-07-01

243

Genetic diversity of loquat germplasm (Eriobotrya japonica (Thunb) Lindl) assessed by SSR markers.  

PubMed

Genetic relationships among 40 loquat (Eriobotrya japonica (Thunb) Lindl) accessions that originated from different countries and that are part of the germplasm collection of the Instituto Valenciano de Investigaciones Agrarias (IVIA) (Valencia, Spain) were evaluated using microsatellites. Thirty primer pairs flanking microsatellites previously identified in Malus x domestica (Borkh.) were assayed. Thirteen of them amplified polymorphic products and unambiguously distinguished 34 genotypes from the 40 accessions analyzed. Six accessions showing identical marker patterns were Spanish local varieties thought to have been derived from 'Algerie' by a mutational process very common in loquat species. A total of 39 alleles were detected in the population studied, with a mean value of 2.4 alleles per locus. The expected and observed heterozygosities were 0.46 and 51% on average, respectively, leading to a negative value of the Wright's fixation index (-0.20). The values of these parameters indicate a smaller degree of genetic diversity in the set of loquat accessions analyzed than in other members of the Rosaceae family. Unweighted pair-group method (UPGMA) cluster analysis, based on Nei's genetic distance, generally grouped genotypes according to their geographic origins and pedigrees. The high number of alleles and the high expected heterozygosity detected with SSR markers developed in Malus x domestica (Borkh.) make them a suitable tool for loquat cultivar identification, confirming microsatellite marker transportability among genera in the Rosaceae family. PMID:15729402

Soriano, José Miguel; Romero, Carlos; Vilanova, Santiago; Llácer, Gerardo; Badenes, María Luisa

2005-02-01

244

Genetic structure of wild emmer wheat populations as reflected by transcribed versus anonymous SSR markers.  

PubMed

Simple sequence repeat (SSR) markers have become a major tool in population genetic analyses. The anonymous genomic SSRs (gSSRs) have been recently supplemented with expressed sequence tag (EST) derived SSRs (eSSRs), which represent the transcribed regions of the genome. In the present study, we used 8 populations of wild emmer wheat (Triticum turgidum subsp. dicoccoides) to compare the usefulness of the two types of SSR markers in assessing allelic diversity and population structure. gSSRs revealed significantly higher diversity than eSSRs in terms of average number of alleles (14.92 vs. 7.4, respectively), polymorphic information content (0.87 vs. 0.68, respectively), and gene diversity (He; 0.55 vs. 0.38, respectively). Despite the overall differences in the level of diversity, Mantel tests for correlations between eSSR and gSSR pairwise genetic distances were found to be significant for each population as well as for all accessions jointly (RM=0.54, p=0.01). Various genetic structure analyses (AMOVA, PCoA, STRUCTURE, unrooted UPGMA tree) revealed a better capacity of eSSRs to distinguish between populations, while gSSRs showed a higher proportion of intrapopulation (among accessions) diversity. We conclude that eSSR and gSSR markers should be employed in conjunction to obtain a high inter- and intra-specific (or inter- and intra-varietal) distinctness. PMID:18356954

Peleg, Zvi; Fahima, Tzion; Abbo, Shahal; Krugman, Tamar; Saranga, Yehoshua

2008-03-01

245

Genetic diversity in basmati rice (Oryza sativa L.) germplasm as revealed by microsatellite (SSR) markers.  

PubMed

Genetic diversity among rice genotypes, including 15 indica basmati advance lines and 5 basmati improved varieties were investigated by 28 SSR markets including one indel marker. The SSRs covered all the 12 chromosomes that distributed across the rice genomes. The mean number of alleles per locus was 3.60, showing average number of polymorphism information content was 0.48. A total of 101 alleles were also identified from the microsatellite marker loci. A number of SSR markers were also identified that could be utilized to differentiate between rice genotypes. Pair wise Nei,s genetic distance between rice genotypes ranged from 0.07 to 0.95. The dendrogram based on cluster analysis by using SSR polymorphism that grouped the 20 genotypes of rice in to five clusters based on their genetic similarity. The result could be useful for the identification and selection of the diverse genotypes for the future cross breeding program and development of new rice varieties. PMID:22567855

Ashfaq, M; Khan, A S

2012-01-01

246

Transferability of STS markers in studying genetic relationships of marvel grass (Dichanthium annulatum).  

PubMed

Transferability of sequence-tagged-sites (STS) markers was assessed for genetic relationships study among accessions of marvel grass (Dichanthium annulatum Forsk.). In total, 17 STS primers of Stylosanthes origin were tested for their reactivity with thirty accessions of Dichanthium annulatum. Of these, 14 (82.4%) reacted and a total 106 (84 polymorphic) bands were scored. The number of bands generated by individual primer pairs ranged from 4 to 11 with an average of 7.57 bands, whereas polymorphic bands ranged from 4 to 9 with an average of 6.0 bands accounts to an average polymorphism of 80.1%. Polymorphic information content (PIC) ranged from 0.222 to 0.499 and marker index (MI) from 1.33 to 4.49. Utilizing Dice coefficient of genetic similarity dendrogram was generated through un-weighted pairgroup method with arithmetic mean (UPGMA) algorithm. Further, clustering through sequential agglomerative hierarchical and nested (SAHN) method resulted three main clusters constituted all accessions except IGBANG-D-2. Though there was intermixing of few accessions of one agro-climatic region to another, largely groupings of accessions were with their regions of collections. Bootstrap analysis at 1000 scale also showed large number of nodes (11 to 17) having strong clustering (> 50). Thus, results demonstrate the utility of STS markers of Stylosanthes in studying the genetic relationships among accessions of Dichanthium. PMID:22471204

Saxena, Raghvendra; Chandra, Amaresh

2011-11-01

247

Genetic diversity analysis of okra (Abelmoschus esculentus L.) by inter-simple sequence repeat (ISSR) markers.  

PubMed

Okra (Abelmoschus esculentus L.) is not only a nutrient-rich vegetable but also an important medicinal herb. Inter-simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and differentiation of 24 okra genotypes. In this study, the PCR products were separated by electrophoresis on 8% nondenaturing polyacrylamide gel and visualized by silver staining. The 22 ISSR primers produced 289 amplified DNA fragments, and 145 (50%) fragments were polymorphic. The 289 markers were used to construct the dendrogram based on the unweighted pair-group method with arithmetic average (UPGMA) cluster analysis. The dendrogram indicated that 24 okras were clustered into 4 geographically distinct groups. The average polymorphism information content (PIC) was 0.531929, which showed that the majority of primers were informative. The high values of allele frequency, genetic diversity, and heterozygosity showed that primer-sample combinations produced measurable fragments. The mean distances ranged from 0.045455 to 0.454545. The dendrogram indicated that the ISSR markers succeeded in distinguishing most of the 24 varieties in relation to their genetic backgrounds and geographical origins. PMID:24841648

Yuan, C Y; Zhang, C; Wang, P; Hu, S; Chang, H P; Xiao, W J; Lu, X T; Jiang, S B; Ye, J Z; Guo, X H

2014-01-01

248

Physical mapping of 49 microsatellite markers on chromosome 19 and correlation with the genetic linkage map  

SciTech Connect

We have regionally localized 49 microsatellite markers developed by Genethon using a panel of previously characterized somatic cell hybrids that retain fragments from chromosome 19. The tight correlation observed between the physical and the genetic orders of the microsatellites provide cytogenetic anchorages to the genetic map data. We propose a position for the centromere just above D19S415, from the study of two hybrids, each of which retains one of the two derivatives of a balanced translocation t(1;19)(q11;q11). Microsatellites, which can be identified by a standard PCR protocol, are useful tools for the localization of disease genes and for the establishment of YAC or cosmid contigs. These markers can also judiciously be used for the characterization of new hybrid cell line panels. We report such a characterization of 11 clones, 8 of which were obtained by irradiation-fusion. Using the whole hybrid panel, we were able to define the order of 12 pairs of genetically colocalized microsatellites. As examples of gene mapping by the combined use of microsatellites and hybrid cell lines, we regionally assigned the PVS locus between the 19q13.2 markers D19S417 and D19S423 and confirmed the locations of fucosyltransferase loci FUT1, FUT2, and FUT5. 13 refs., 1 fig.

Reguigne-Arnould, I.; Mollicone, R.; Candelier, J.J. [INSERM, Villejuif (France)] [and others] [INSERM, Villejuif (France); and others

1996-03-05

249

Genetic differentiation between natural and hatchery populations of Manila clam (Ruditapes philippinarum) based on microsatellite markers.  

PubMed

Manila clam (Ruditapes philippinarum) is one of the major aquaculture species around the world and supports an important segment of the aquaculture industry in China. In this study, we used ten microsatellite markers to detect genetic diversity within six R. philippinarum populations and genetic differentiation between them. A total of 109 alleles were detected across all loci. Compared to wild populations (N(A) = 8.4-9.1 alleles/locus, H(E) = 0.75-0.77, H(O) = 0.67-0.73), hatchery stocks showed less genetic variation as revealed in lower number of alleles and lower heterozygosity (N(A) = 7.4-7.5 alleles/locus, H(E) = 0.72-0.75, H(O) = 0.68-0.70), indicating that a bottleneck effect has occurred in hatchery history. Significant genetic differentiation was observed between cultured stocks (P < 0.05), and between cultured and wild populations (P < 0.05). Phylogenetic analysis showed a clear separation of the northern three populations and the southern three populations, suggesting that geographically separated populations of R. philippinarum could be genetically differentiated with limited genetic information exchanged between them. The information obtained in this study indicates that the northern and southern populations of R. philippinarum should be managed separately in hatchery practices for the preservation of genetic diversity in wild populations. PMID:24535849

Xing, K; Gao, M L; Li, H J

2014-01-01

250

Towards genetic markers in animal populations as biomonitors for human-induced environmental change.  

PubMed

Genetic markers provide potentially sensitive indicators of changes in environmental conditions because the genetic constitution of populations is normally altered well before populations become extinct. Genetic indicators in populations include overall genetic diversity, genetic changes in traits measured at the phenotypic level, and evolution at specific loci under selection. While overall genetic diversity has rarely been successfully related to environmental conditions, genetically based changes in traits have now been linked to the presence of toxins and both local and global temperature shifts. Candidate loci for monitoring stressors are emerging from information on how specific genes influence traits, and from screens of random loci across environmental gradients. Drosophila research suggests that chromosomal regions under recent intense selection can be identified from patterns of molecular variation and a high frequency of transposable element insertions. Allele frequency changes at candidate loci have been linked to pesticides, pollutants and climate change. Nevertheless, there are challenges in interpreting allele frequencies in populations, particularly when a large number of loci control a trait and when interactions between alleles influence trait expression. To meet these challenges, population samples should be collected for longitudinal studies, and experimental programmes should be undertaken to link variation at candidate genes to ecological processes. PMID:17204118

Hoffmann, Ary A; Daborn, Phillip J

2007-01-01

251

Genetic differences among Vietnamese Haplorchis taichui populations using the COI genetic marker.  

PubMed

Adults of the fish-borne intestinal trematode species Haplorchis taichui were collected from humans in three provinces of Vietnam: Ha Giang, Thanh Hoa and Quang Tri. Genetic analysis revealed three groups of the parasite from clustering dendrograms, correlating with the localities in which they were collected. Measurements of evolutionary divergence over sequence pairs were greater between the different populations than within them, which indicated that the three populations were genetically different. The significance (Fst= 0.73; P value < 0.05) of the genetic variation of the three studied populations implied that genetic separation of the populations had already occurred, which may have been caused by a low gene flow among the different H. taichui populations. Factors contributing to the low gene flow may include isolation resulting from the intermediate-host fish rarely being sold outside of the rural commune where they are raised and the enclosed aquacultural areas themselves. PMID:22309996

Dung, D T; Hop, N T; Thaenkham, U; Waikagul, J

2013-03-01

252

Molecular Markers for Biomass Traits: Association, Interaction and Genetic Divergence in Silkworm Bombyx mori  

PubMed Central

Improvement of high yielding, disease resistant silkworm strains became imminent to increase production of silk, which is a major revenue earner for sericulturists. Since environment interacts with phenotype, conventional breeding did not result in commendable yield improvement in synthetic strains of silkworm, Bombyx mori. Identification of DNA markers associated with different economically important biomass traits and its introgression could assist molecular breeding and expression of stabilized high yielding characters, but genetic basis of most quantitative traits in silkworm is poorly understood due to its polygenic control. Correlation analysis (R = 0.9) revealed significant interrelation among biomass traits viz., larval duration (TLD), larval weight (LWT), cocoon weight (CWT), shell weight (SWT), shell ratio (SR) and floss content. PCR using inter simple sequence repeat (ISSR) primers revealed 92% polymorphism among 14 tropical and temperate strains of B. mori, with average diversity index of 0.747. Stepwise multiple regression analysis (MRA) selected 35 ISSR markers positively or negatively correlated with different biomass traits, illustrated polygenic control. ISSR marker 830.81050bp was significantly associated with LWT, CWT, SWT, SR and floss content, indicated its pleiotropic role. Two ISSR markers, 835.51950bp and 825.9710bp showed significant association with floss content and TLD. These markers were segregated in F2 generation and Chi-square test confirmed (?2 = ~45; P < 0.05) its genetic contribution to the associated biomass traits. Strains, with both positively and negatively correlated markers, had intermediate mean value for biomass traits (eg. SWT = 0.17 ± 0.014 g in GNM and Moria) indicated interaction of loci in natural populations. Low yielding Indian strains grouped together by Hierarchical clustering. Chinese and Japanese strains were distributed in the periphery of ALSCAL matrix indicated convergence of genetic characters in Indian strains. Average genetic distance between Chinese strains and Indian strains (0.193) significantly (P < 0.01) varied from that between Chinese and Japanese strains. Interaction of loci and allelic substitutions induced phenotypic plasticity in temperate B. mori populations on tropic adaptation in India. These outcomes show possibility to combine favorable alleles at different QTL to increase larval, cocoon and shell weight.

Pradeep, Appukuttannair R; Jingade, Anuradha H; Urs, Raje S

2007-01-01

253

Epidemiological association of Campylobacter jejuni groups with pathogenicity-associated genetic markers  

PubMed Central

Background Campylobacter jejuni, the most leading cause for bacterial gastroenteritis worldwide, shows a high genetic diversity among its isolates. Recently, we demonstrated the existence of six C. jejuni-groups by combining MLST with six genetic markers. These groups were further characterized by the detection of cj1321-cj1326, fucP, cj0178, cj0755/cfrA, ceuE, pldA, cstII, and cstIII in order (I.) to show further associations between these different genetic markers and MLST CCs. Moreover, different studies were able to associate several of these markers: a sialylated lipoologosaccharide (cstII/III+), the gamma-glytamyl-transpeptidase (ggt+), and the absence of a certain allele of the enterochelin-uptake-binding-protein (ceuE11168-) with severe campylobacteriosis, bloody diarrhea and unpleasant outcome. Additionally more than half of human Campylobacter-isolates were assigned to a non-livestock clade associated with the absence of cj1321-cj1326. These isolates were considered as mere colonizers. From the combination of marker genes, the ratio of human isolates in a specific group, and clinical data (II.) it should be demonstrated to which of the previous defined groups these Campylobacter-subpopulations, associated with higher virulence, correspond. Results Besides the marker gene pldA, all new estimated genetic markers show significant differences in their distribution among the various MLST-based groups. Especially the genes for cj1321-cj1326, fucP, cj0178, cj0755/cfrA are widely associated with each other and split the study population into two major and seven intermediate groups substantiating the previous group-definition, whereas cstII and cstIII indicate at least three groups following an independent distribution pattern. Conclusions Based on these data a group of C. jejuni-isolates characterized by the presence of ansB, dmsA, ggt, and the absence of cj1365c, cj1585c, cj1321-cj1326, fucP, cj0178, cj0755/cfrA, and cstII/III was associated with a higher prevalence in human campylobacteriosis, bloody diarrhea as well as hospitalization and bears obviously a higher virulence for humans. In contrast to that better livestock-adapted groups characterized by the ability to utilize L-fucose and the presence of all of the five identified putative C. jejuni iron-uptake systems as well as cj1321-cj1326, cj1365c, cj1585c, and cstII and/or cstIII (sialylated lipoologosaccharide) is more prevalent in animal hosts and was secondary associated with less severe campylobacteriosis.

2012-01-01

254

Molecular Markers for Biomass Traits: Association, Interaction and Genetic Divergence in Silkworm Bombyx mori.  

PubMed

Improvement of high yielding, disease resistant silkworm strains became imminent to increase production of silk, which is a major revenue earner for sericulturists. Since environment interacts with phenotype, conventional breeding did not result in commendable yield improvement in synthetic strains of silkworm, Bombyx mori. Identification of DNA markers associated with different economically important biomass traits and its introgression could assist molecular breeding and expression of stabilized high yielding characters, but genetic basis of most quantitative traits in silkworm is poorly understood due to its polygenic control. Correlation analysis (R = 0.9) revealed significant interrelation among biomass traits viz., larval duration (TLD), larval weight (LWT), cocoon weight (CWT), shell weight (SWT), shell ratio (SR) and floss content. PCR using inter simple sequence repeat (ISSR) primers revealed 92% polymorphism among 14 tropical and temperate strains of B. mori, with average diversity index of 0.747. Stepwise multiple regression analysis (MRA) selected 35 ISSR markers positively or negatively correlated with different biomass traits, illustrated polygenic control. ISSR marker 830.8(1050bp) was significantly associated with LWT, CWT, SWT, SR and floss content, indicated its pleiotropic role. Two ISSR markers, 835.5(1950bp) and 825.9(710bp) showed significant association with floss content and TLD. These markers were segregated in F(2) generation and Chi-square test confirmed (chi(2) = ~45; P < 0.05) its genetic contribution to the associated biomass traits. Strains, with both positively and negatively correlated markers, had intermediate mean value for biomass traits (eg. SWT = 0.17 +/- 0.014 g in GNM and Moria) indicated interaction of loci in natural populations. Low yielding Indian strains grouped together by Hierarchical clustering. Chinese and Japanese strains were distributed in the periphery of ALSCAL matrix indicated convergence of genetic characters in Indian strains. Average genetic distance between Chinese strains and Indian strains (0.193) significantly (P < 0.01) varied from that between Chinese and Japanese strains. Interaction of loci and allelic substitutions induced phenotypic plasticity in temperate B. mori populations on tropic adaptation in India. These outcomes show possibility to combine favorable alleles at different QTL to increase larval, cocoon and shell weight. PMID:19662204

Pradeep, Appukuttannair R; Jingade, Anuradha H; Urs, Raje S

2007-01-01

255

Use of transferable Nicotiana tabacum L. microsatellite markers for investigating genetic diversity in the genus Nicotiana.  

PubMed

The recent development of microsatellite markers for tobacco, Nicotiana tabacum L., may be valuable for genetic studies within the genus Nicotiana. The first objective was to evaluate transferability of 100 N. tabacum microsatellite primer combinations to 5 diploid species closely related to tobacco. The number of primer combinations that amplified scorable bands in these species ranged from 42 to 56. Additional objectives were to assess levels of genetic diversity amongst available accessions of diploid relatives closely related to tobacco (species of sections Sylvestres and Tomentosae), and to evaluate the efficacy of microsatellite markers for establishing species relationships in comparison with existing phylogenetic reconstructions. A subset of 46 primer combinations was therefore used to genotype 3 synthetic tobaccos and an expanded collection of 51 Nicotiana accessions representing 15 species. The average genetic similarity for 7 diverse accessions of tobacco was greater than the average similarity for N. otophora accessions, but lower than the average genetic similarities for N. sylvestris, N. tomentosa, N. kawakamii, and N. tomentosiformis accessions. A microsatellite-based phylogenetic tree was largely congruent with taxonomic representations based on morphological, cytological, and molecular observations. Results will be useful for selection of parents for creation of diploid mapping populations and for germplasm introgression activities. PMID:18650945

Moon, H S; Nicholson, J S; Lewis, R S

2008-08-01

256

[Genetic variability of Siberian fir (Abies sibirica Ledeb.) inferred from AFLP markers].  

PubMed

Genetic variability of AFLP markers was studied in 20 populations of Siberian fir (Abies sibirica (Pinaceae) and in two populations of Far-Eastern Manchurian fir A. nephrolepis and Sakhalin fir A. sachalinensis each. Four pairs of selective primers were used. In total, 168 samples from three fir species were genotyped for 117 polymorphic loci. According to the AMOVA results, the variability proportion characterizing the differences between three Abies species was several times higher (F(CT) = 0.53) than that accounting for among-population differences within the species (F(SC) = 0.125). Differentiation of the A. sibirica populations based on AFLP markers exceeded 14% (F(ST) = 0.141). Significant correlation between the genetic distances calculated from the AFLP data and the geographic distances between populations was found. The results of AFLP variability analysis supported and supplemented the conclusions inferred previously from allozyme and cpSSR data: several genetically similar geographic groups of Siberian fir were identified. These groups differ both in allele frequencies and in the levels of genetic variation. PMID:21516799

Semerikova, S A; Semerikov, V L

2011-02-01

257

Selected Genetic Markers of Blood and Secretions for Youths, 12-17 Years of Age, United States.  

National Technical Information Service (NTIS)

Percentage distributions of nine genetic markers, including ABO blood type, secretor ability, haptoglobin type, transferrin type, and group specific component type, are presented and discussed by age, sex, race, geographic region, family income and parent...

B. H. Cohen W. B. Bias P. V. V. Hamill T. A. Drizd E. L. Diamond

1980-01-01

258

Physical and genetic mapping of the serpin gene cluster at 14q32. 1: Allelic association and a unique haplotype associated with [alpha][sub 1]-antitrypsin deficiency  

SciTech Connect

The [alpha][sub 1]-antitrypsin (PI) gene is part of a cluster of structurally related serine protease inhibitor genes localized at chromosome 14q32, a cluster that includes the [alpha][sub 1]-anticymotrypsin (AACT), protein C inhibitor (PCI), and corticosteroid-binding globulin (CBG) genes and the [alpha][sub 1]-antitrypsin-like pseudogene (PIL). The order of the genes is refined here by genetic mapping using simple tandem repeat polymorphisms (STRPs) and by physical mapping in YACs. The order of the genes is (cetromere)-CBG-PIL-PI-PCI-AACT-(telomere). Analysis of DNA haplotypes comprising STRP and RFLP markers in the serpin genes reveals considerable allelic association throughout the cluster. Furthermore, the common [alpha][sub 1]-antitrypsin deficiency allele, PI[sup *]Z, has a unique DNA haplotype at the CBG, PIL, and PI loci, which extends over 60 kb in 97% of cases and in 44% of cases includes the PCI and AACT loci. This unique haplotype will be of use in examining a number of other diseases, particularly those with an inflammatory component, thought to be associated with [alpha][sub 1]-antitrypsin deficiency or partial deficiency. 23 refs., 6 figs., 4 tabs.

Byth, B.C.; Billingsley, G.D.; Cox, D.W. (Hospital for Sick Children, Toronto, Ontario (Canada))

1994-07-01

259

Genetic diversity analysis of BMY cattle based on microsatellite DNA markers.  

PubMed

BMY cattle (1/2 Brahman, 1/4 Murray Grey and 1/4 Yunnan Yellow cattle) has been inter se breeding since 1980s. Genetic diversity of BMY cattle was extensively investigated using 16 microsatellite markers. A total of 130 microsatellite alleles and high allele size variance were detected. All loci displayed high genetic diversity with overall mean of N(a) = 8.13, PIC = 0.7224 and H(e) = 0.7666, which were higher than those of many other beef breeds. The allele-sharing neighbour-joining tree clearly displayed the new genotypic combinations and the minglement from both BMY cattle and Brahman. The results provided the genetic information to match the standards of new beef breed in South China. PMID:22730772

Qu, K X; Huang, B Z; Yang, G R; He, Z X; Zhang, Y P; Zan, L S

2012-04-01

260

Microsatellite Markers to Determine Population Genetic Structure in the Golden Anchovy, Coilia dussumieri.  

PubMed

Coilia dussumieri (Valenciennes, 1848) commonly called as golden anchovy, constitutes a considerable fishery in the northern part of both the west and east coasts of India. Despite its clear-cut geographic isolation, the species is treated as a unit stock for fishery management purposes. We evaluated 32 microsatellite primer pairs from three closely related species (resource species) belonging to the family Engraulidae through cross-species amplification in C. dussumieri. Successful cross-priming was obtained with 10 loci, which were sequenced for confirmation of repeats. Loci were tested for delineating the genetic stock structure of four populations of C. dussumieri from both the coasts of India. The number of alleles per locus ranged from 8 to 18, with a mean of 12.3. Results of pairwise F ST indicated genetic stock structuring between the east and west coast populations of India and also validated the utilization of identified microsatellite markers in population genetic structure analysis. PMID:24619789

Kathirvelpandian, A; Gopalakrishnan, A; Lakra, W S; Krishna, Gopal; Sharma, Rupam; Musammilu, K K; Basheer, V S; Jena, J K

2014-06-01

261

Questionable Specificity of Genetic Total Faecal Pollution Markers for Integrated Water Quality Monitoring and Source Tracking  

NASA Astrophysics Data System (ADS)

Characterisation of microbial faecal hazards in water is a fundamental aspect for target-orientated water resources management to achieve appropriate water quality for various purposes like water supply or agriculture and thus to minimize related health risks. Nowadays the management of water resources increasingly demands detailed knowledge on the extent and the origin of microbial pollution. Cultivation of standard faecal indicator bacteria, which has been used for over a century to test the microbiological water quality, cannot sufficiently meet these challenges. The abundant intestinal bacterial populations are very promising alternative targets for modern faecal indication systems. Numerous assays for the detection of genetic markers targeting source-specific populations of the phylum Bacteroidetes have been developed in recent years. In some cases markers for total faecal pollution were also proposed in order to relate source-specific marker concentrations to general faecal pollution levels. However, microbial populations in intestinal and non-intestinal systems exhibit a dazzling array of diversity and molecular analysis of microbial faecal pollution has been based on a fragmentary puzzle of very limited sequence information. The aim of this study was to test the available qPCR-based methods detecting genetic Bacteroidetes markers for total faecal pollution in terms of their value and specificity as indicators of faecal pollution. We applied the AllBac (Layton et al., 2006) the BacUni (Kildare et al., 2007) and the Bacteroidetes (Dick and Field, 2004) assays on soil DNA samples. Samples were collected in well characterised karst spring catchments in Austria's Eastern Calcareous Alps. They were at various levels of altitude between 800 and 1800 meters above sea level and from several different habitats (woodland, alpine pastures, krummholz). In addition we tried to choose sampling sites representing a presumptive gradient of faecal pollution levels. For example sites with obvious faecal influence (e.g. right next to a cowpat) were included as well as more pristine sites without faecal influence from large animals (e.g. fenced areas). Surprisingly, results from investigations with the AllBac assay showed concentrations of the total faecal marker in soil in the range of 106 to 109 Marker Equivalents per g of soil, which is equal or only slightly lower than the concentrations of this particular marker in faeces or raw sewage. Preliminary results from the other tested assays seem to confirm that the targeted markers are also highly abundant in soils. In addition, the markers were present in comparable concentrations in soils from pristine locations as well as in soils under the potential influence of faeces giving a strong indication that these methods also target non-intestinal, autochthonous soil populations. In contrast, source-specific markers (ruminant-specific BacR and human-specific BacH, Reischer et al., 2007, 2006) could only be detected in 30 to 50% of the soil samples at concentrations close to the detection limit, which is at least four orders of magnitude lower than in faecal samples of the respective target sources, ruminant animals and humans. The achieved results call the applicability of the proposed qPCR-based assays for total faecal pollution into question. In fact the assays do not seem to be specific for intestinal Bacteroidetes populations at all and the respective marker concentration levels in pristine soils negate their applicability in the investigated areas. This study also emphasizes the need to test the specificity and sensitivity of qPCR-based assays for total faecal pollution on the local level and especially against non-intestinal environmental samples, which might contribute to marker levels in the aquatic compartment. In conclusion there is a strong demand for marker-based detection techniques for total faecal pollution in water quality monitoring and risk assessment but currently none of the tested assays seems to meet the methodical requirements.

Vierheilig, Julia; Reischer, Georg H.; Farnleitner, Andreas H.

2010-05-01

262

Genetic diversity and population structure of Chinese pony breeds using microsatellite markers.  

PubMed

China is one of the principal origins of ponies in the world. We made a comprehensive analysis of genetic diversity and population structure of Chinese ponies based on 174 animals of five indigenous Chinese pony breeds from five provinces using 13 microsatellite markers. One hundred and forty-four alleles were detected; the mean number of effective alleles among the pony breeds ranged from 5.38 (Guizhou) to 6.78 (Sichuan); the expected heterozygosity ranged from 0.82 (Guizhou) to 0.85 (Debao, Sichuan). Although abundant genetic variation was found, the genetic differentiation was low between the ponies, with 6% total genetic variance among the different breeds. All the pairwise F(ST) values were significant; they varied from 0.0424 for the Sichuan-Yunnan pair to 0.0833 for the Guizhou-Sichuan pair. All five pony breeds deviated from Hardy-Weinberg equilibrium, except the Yunnan pony. Phylogenetic trees of the five pony breeds based on genetic distances were constructed using a neighbor-joining method. The Sichuan and Yunnan ponies were grouped into the same branch, with a high bootstrap support value (97%). Guizhou and Ningqiang ponies were clustered into the same branch with a bootstrap value of 56%, whereas the Debao pony was placed in a separate group, with a bootstrap value of 56%. This grouping pattern was supported by genetic structure analysis. PMID:22782636

Xu, L X; Yang, S L; Lin, R Y; Yang, H B; Li, A P; Wan, Q S

2012-01-01

263

Estimating black bear population density and genetic diversity at Tensas River, Louisiana using microsatellite DNA markers  

USGS Publications Warehouse

The Recovery Plan for the federally threatened Louisiana black bear (Ursus americanus luteolus) mandates that remnant populations be estimated and monitored. In 1999 we obtained genetic material with barbed-wire hair traps to estimate bear population size and genetic diversity at the 329-km2 Tensas River Tract, Louisiana. We constructed and monitored 122 hair traps, which produced 1,939 hair samples. Of those, we randomly selected 116 subsamples for genetic analysis and used up to 12 microsatellite DNA markers to obtain multilocus genotypes for 58 individuals. We used Program CAPTURE to compute estimates of population size using multiple mark-recapture models. The area of study was almost entirely circumscribed by agricultural land, thus the population was geographically closed. Also, study-area boundaries were biologically discreet, enabling us to accurately estimate population density. Using model Chao Mh to account for possible effects of individual heterogeneity in capture probabilities, we estimated the population size to be 119 (SE=29.4) bears, or 0.36 bears/km2. We were forced to examine a substantial number of loci to differentiate between some individuals because of low genetic variation. Despite the probable introduction of genes from Minnesota bears in the 1960s, the isolated population at Tensas exhibited characteristics consistent with inbreeding and genetic drift. Consequently, the effective population size at Tensas may be as few as 32, which warrants continued monitoring or possibly genetic augmentation.

Boersen, M. R.; Clark, J. D.; King, T. L.

2003-01-01

264

Genetic diversity of Lagerstroemia (Lythraceae) species assessed by simple sequence repeat markers.  

PubMed

Lagerstroemia (crape myrtle) are famous ornamental plants with large pyramidal racemes, long flower duration, and diverse colors. However, little is known about the genetic structure and diversity of germplasm in Lagerstroemia. We genotyped 81 L. indica cultivars, five other species of Lagerstroemia, and 10 interspecific hybrids using 30 simple sequence repeat markers; 275 alleles were generated with a mean of nine alleles per locus. The mean polymorphism information content value, a measure of gene diversity, was 0.63, with a range from 0.25 to 0.86. The mean observed heterozygosity (0.51) tended to be lower than the mean expected heterozygosity (0.67). The mean F-statistics (F(ST), F(IS), and F(IT)) were 0.05, 0.20, and 0.24, respectively, indicating a high level of genetic variation among cultivars. Clustering analysis based on genetic distance divided the 96 genotypes into three distinct groups, which corresponded with their genetic backgrounds and geographic regions. L. indica cultivars and the other five L. species were grouped into different sub-clusters. Chinese and North American cultivars were divided into different clusters. These data about the genetic relationship among cultivars demonstrated the potential value of L. indica cultivars and other Lagerstroemia species for widening the genetic basis of breeding programs for this ornamental flower. PMID:23079847

He, D; Liu, Y; Cai, M; Pan, H T; Zhang, Q X; Wang, X Y; Wang, X J

2012-01-01

265

Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map.  

PubMed

To obtain more information on the Hevea brasiliensis genome, we sequenced the transcriptome from the vegetative shoot apex yielding 2 311 497 reads. Clustering and assembly of the reads produced a total of 113 313 unique sequences, comprising 28 387 isotigs and 84 926 singletons. Also, 17 819 expressed sequence tag (EST)-simple sequence repeats (SSRs) were identified from the data set. To demonstrate the use of this EST resource for marker development, primers were designed for 430 of the EST-SSRs. Three hundred and twenty-three primer pairs were amplifiable in H. brasiliensis clones. Polymorphic information content values of selected 47 SSRs among 20 H. brasiliensis clones ranged from 0.13 to 0.71, with an average of 0.51. A dendrogram of genetic similarities between the 20 H. brasiliensis clones using these 47 EST-SSRs suggested two distinct groups that correlated well with clone pedigree. These novel EST-SSRs together with the published SSRs were used for the construction of an integrated parental linkage map of H. brasiliensis based on 81 lines of an F1 mapping population. The map consisted of 97 loci, consisting of 37 novel EST-SSRs and 60 published SSRs, distributed on 23 linkage groups and covered 842.9 cM with a mean interval of 11.9 cM and ?4 loci per linkage group. Although the numbers of linkage groups exceed the haploid number (18), but with several common markers between homologous linkage groups with the previous map indicated that the F1 map in this study is appropriate for further study in marker-assisted selection. PMID:22086998

Triwitayakorn, Kanokporn; Chatkulkawin, Pornsupa; Kanjanawattanawong, Supanath; Sraphet, Supajit; Yoocha, Thippawan; Sangsrakru, Duangjai; Chanprasert, Juntima; Ngamphiw, Chumpol; Jomchai, Nukoon; Therawattanasuk, Kanikar; Tangphatsornruang, Sithichoke

2011-12-01

266

Transcriptome Sequencing of Hevea brasiliensis for Development of Microsatellite Markers and Construction of a Genetic Linkage Map  

PubMed Central

To obtain more information on the Hevea brasiliensis genome, we sequenced the transcriptome from the vegetative shoot apex yielding 2 311 497 reads. Clustering and assembly of the reads produced a total of 113 313 unique sequences, comprising 28 387 isotigs and 84 926 singletons. Also, 17 819 expressed sequence tag (EST)-simple sequence repeats (SSRs) were identified from the data set. To demonstrate the use of this EST resource for marker development, primers were designed for 430 of the EST-SSRs. Three hundred and twenty-three primer pairs were amplifiable in H. brasiliensis clones. Polymorphic information content values of selected 47 SSRs among 20 H. brasiliensis clones ranged from 0.13 to 0.71, with an average of 0.51. A dendrogram of genetic similarities between the 20 H. brasiliensis clones using these 47 EST-SSRs suggested two distinct groups that correlated well with clone pedigree. These novel EST-SSRs together with the published SSRs were used for the construction of an integrated parental linkage map of H. brasiliensis based on 81 lines of an F1 mapping population. The map consisted of 97 loci, consisting of 37 novel EST-SSRs and 60 published SSRs, distributed on 23 linkage groups and covered 842.9 cM with a mean interval of 11.9 cM and ?4 loci per linkage group. Although the numbers of linkage groups exceed the haploid number (18), but with several common markers between homologous linkage groups with the previous map indicated that the F1 map in this study is appropriate for further study in marker-assisted selection.

Triwitayakorn, Kanokporn; Chatkulkawin, Pornsupa; Kanjanawattanawong, Supanath; Sraphet, Supajit; Yoocha, Thippawan; Sangsrakru, Duangjai; Chanprasert, Juntima; Ngamphiw, Chumpol; Jomchai, Nukoon; Therawattanasuk, Kanikar; Tangphatsornruang, Sithichoke

2011-01-01

267

RFLP Markers Show Genetic Recombination in Botryotinia fuckeliana (Botrytis cinerea) and Transposable Elements Reveal Two Sympatric Species  

Microsoft Academic Search

Molecular markers revealed that Botryotinia jiickeliana (the teleomorph of Botrytis cinerea), a haploid, filamentous, heterothallic ascomycete, contained a large amount of intrapopulation genetic variation. The markers were used to determine the mode of reproduction and the population structure of this fungus. We did not detect any differentiation between isolates from different organs, collection dates, varieties of grape, or locations in

Tatiana Giraud; Dominique Fortini; Caroline Levis; Pierre Leroux; Yves Brygoo

268

Hierarchical Analysis of Genetic Structure in Native Fire Ant Populations: Results From Three Classes of Molecular Markers  

Microsoft Academic Search

We describe genetic structure at various scales in native populations of the fire ant Solenopsis invicta using two classes of nuclear markers, allozymes and microsatellites, and markers of the mitochondrial genome. Strong structure was found at the nest level in both the monogyne (single queen) and polygyne (multiple queen) social forms using allozymes. Weak but significant microgeographic structure was detected

Kenneth G. Ross; Michael J. B. Krieger; D. DeWayne Shoemaker; Edward L. Vargos; Laurent Kellert

1997-01-01

269

Analysis of a Detailed Genetic Linkage Map of Lactuca sativa (Lettuce) Constructed From RFLP and RAPD Markers  

Microsoft Academic Search

A detailed genetic map has been constructed from the F, population of a single intraspecific cross of Lactuca sativa (n = 9). It comprises 319 loci, including 152 restriction fragment length polymorphism (RFLP), 130 random amplified polymorphic DNA (RAPD), 7 isozyme, 19 disease resistance, and 11 morphological markers. Thirteen major, four minor linkage groups and several unlinked markers are identified

Rick V. Kesseli; Pt Ilan Parant; Richard W. Michelmore

270

Assessment of genetic diversity of wheat genotypes by resistance gene analog-EST markers.  

PubMed

Resistance gene analog-expressed sequence tag (RGA-EST)-based markers have been used for variety discrimination and studies of genetic diversity in wheat. Our aim is to increase the competitiveness of public wheat breeding programs through intensive use of modern selection technologies, mainly marker-assisted selection. The genetic diversity of 77 wheat nucleotide binding site (NBS)-containing RGA-ESTs was assessed. Resistant and susceptible bread wheat (Triticum aestivum) genotypes were used as sources of DNA for PCR amplifications. In our previous studies, the F? individuals derived from the combinations PI178383 x Harmankaya99, Izgi2001 x ES14, and Sonmez2001 x Aytin98 were evaluated for yellow rust resistance at both seedling and adult stages to identify DNA markers. We have now examined the genetic variability among the resistant and susceptible Turkish wheat cultivars for yellow rust disease and the mean genetic distance between the cultivars. The highest similarity was 0.500 between Harmankaya99 and Sonmez2001. The lowest similarity was 0.286 between Aytin98, PI178383 and Aytin98, ES14. A relatively high level (49.5%) of polymorphism was observed with 77 RGA-EST primers across the six wheat genotypes, despite the fact that all of them were local cultivars from geographically close locations. RGA-EST sequences were compared by BlastX algorithms for amino acid sequences to determine the polymorphic categories among the combinations. BlastX analyses of six RGA-ESTs that gave polymorphic patterns for all combinations were NBS-LRR class RGA, NB-ARC domain containing protein, NBS-type resistance protein RGC5, NBS-LRR-S/ TPK stem rust resistance protein, and putative MLA1 proteins, while 38 RGA-EST gave a monomorphic pattern. PMID:21710462

Karakas, O; Gurel, F; Uncuoglu, A A

2011-01-01

271

Genetic ancestry inference using support vector machines, and the active emergence of a unique American population  

PubMed Central

We use genotype data from the Marshfield Clinical Research Foundation Personalized Medicine Research Project to investigate genetic similarity and divergence between Europeans and the sampled population of European Americans in Central Wisconsin, USA. To infer recent genetic ancestry of the sampled Wisconsinites, we train support vector machines (SVMs) on the positions of Europeans along top principal components (PCs). Our SVM models partition continent-wide European genetic variance into eight regional classes, which is an improvement over the geographically broader categories of recent ancestry reported by personal genomics companies. After correcting for misclassification error associated with the SVMs (<10%, in all cases), we observe a >14% discrepancy between insular ancestries reported by Wisconsinites and those inferred by SVM. Values of FST as well as Mantel tests for correlation between genetic and European geographic distances indicate minimal divergence between Europe and the local Wisconsin population. However, we find that individuals from the Wisconsin sample show greater dispersion along higher-order PCs than individuals from Europe. Hypothesizing that this pattern is characteristic of nascent divergence, we run computer simulations that mimic the recent peopling of Wisconsin. Simulations corroborate the pattern in higher-order PCs, demonstrate its transient nature, and show that admixture accelerates the rate of divergence between the admixed population and its parental sources relative to drift alone. Together, empirical and simulation results suggest that genetic divergence between European source populations and European Americans in Central Wisconsin is subtle but already under way.

Haasl, Ryan J; McCarty, Catherine A; Payseur, Bret A

2013-01-01

272

Application of Microsatellite Markers in Conservation Genetics and Fisheries Management: Recent Advances in Population Structure Analysis and Conservation Strategies  

PubMed Central

Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management.

Abdul-Muneer, P. M.

2014-01-01

273

Can Coronene and/or Benzo(a)pyrene/Coronene ratio act as unique markers for vehicle emission?  

PubMed

Coronene is a high molecular weight polycyclic aromatic hydrocarbon with seven aromatic rings. It, more specifically a lower ratio of Benzo[a]pyrene to Coronone (BaP/COR), is suggested as a marker for vehicle emission. In the present study, emissions of Coronene were measured from residential combustions of wood, crop straw, and pellets. The detection of COR in non-vehicle emission sources, and comparable BaP/COR ratios between the solid fuel combustion and vehicle emissions indicated that the generality of COR or the BaP/COR ratio as markers for the vehicle emission would be questionable, especially for the area where solid fuel combustion dominated the PAHs emission. PMID:24048010

Shen, Guofeng; Chen, Yuanchen; Wei, Siye; Fu, Xiaofang; Ding, Aijun; Wu, Haisuo; Tao, Shu

2014-01-01

274

Microsatellite and minisatellite markers based DNA fingerprinting and genetic diversity of blast and ufra resistant genotypes.  

PubMed

A total of 78 alleles and 29 loci were detected from nine microsatellite and three minisatellite markers, respectively across 26 blast and ufra disease resistant genotypes. For blast resistant genotypes, the Polymorphic Information Content (PIC) values ranged from 0.280 to 0.726 and RM21 was considered as the best marker. PIC values ranged from 0.5953 to 0.8296 for ufra resistant genotypes and RM23 was the best marker for characterization of ufra resistant genotypes. The genetic similarity analysis using UPGMA clustering generated nine clusters with coefficient of 0.66 for blast resistant genotypes while five genetic clusters with similarity coefficient of 0.42 for ufra resistant genotypes. In order to develop resistant varieties of two major diseases of rice, hybridisation should be made using the parents, BR29 and NJ70507, BR36 and NJ70507 for blast, while BR11 and Aokazi, BR3 and Aokazi, Rayda and BR3 and Rayda and BR11 for ufra. PMID:21513897

Latif, M A; Rafii Yusop, Mohd; Motiur Rahman, M; Bashar Talukdar, M R

2011-04-01

275

Plant domestication, a unique opportunity to identify the genetic basis of adaptation  

PubMed Central

Despite the fundamental role of plant domestication in human history and the critical importance of a relatively small number of crop plants to modern societies, we still know little about adaptation under domestication. Here we focus on efforts to identify the genes responsible for adaptation to domestication. We start from a historical perspective, arguing that Darwin's conceptualization of domestication and unconscious selection provides valuable insight into the evolutionary history of crops and also provides a framework to evaluate modern methods used to decipher the genetic mechanisms underlying phenotypic change. We then review these methods, framing the discussion in terms of the phenotype–genotype hierarchy. Top-down approaches, such as quantitative trait locus and linkage disequilibrium mapping, start with a phenotype of interest and use genetic analysis to identify candidate genes. Bottom-up approaches, alternatively, use population genetic analyses to identify potentially adaptive genes and then rely on standard bioinformatics and reverse genetic tools to connect selected genes to a phenotype. We discuss the successes, advantages, and challenges of each, but we conclude that bottom-up approaches to understanding domestication as an adaptive process hold greater promise both for the study of adaptation and as a means to identify genes that contribute to agronomically important traits.

Ross-Ibarra, Jeffrey; Morrell, Peter L.; Gaut, Brandon S.

2007-01-01

276

Developing regional genetic counseling for southern Chinese with nonsyndromic hearing impairment: a unique mutational spectrum  

PubMed Central

Background Racial and regional factors are important for the clinical diagnosis of non-syndromic hearing impairment. Comprehensive genetic analysis of deaf patients in different regions of China must be performed to provide effective genetic counseling. To evaluate the mutational spectrum of south Chinese families, we performed genetic analysis for non-syndromic hearing impairment in this population. Methods Complete clinical evaluations were performed on 701 unrelated patients with non-syndromic hearing impairment from six provinces in south China. Each subject was screened for common mutations, including SLC26A4 c.IVS7-2A?>?G, c.2168A?>?G; mitochondrial DNA m.1555A?>?G, m.1494C?>?T, m.7444G?>?A, m.7445A?>?G; GJB3 c.538C?>?T, c.547G?>?A; and WFS1 c.1901A?>?C, using pyrosequencing. GJB2 and SLC26A4 coding region mutation detection were performed using Sanger sequencing. Results Genetic analysis revealed that among the etiology of non-syndromic hearing impairment, GJB2, SLC26A4, and mitochondrial m.1555A?>?G mutations accounted for 18.0%, 13.1%, and 0.9%, respectively. Common mutations included GJB2 c.235delC, c.109G?>?A, SLC26A4 c.IVS7-2A?>?G, c.1229 T?>?C, and mitochondrial m.1555A?>?G. The total mutation rate was 45.1% in all patients examined in south China. Overall, the clear contribution of GJB2, SLC26A4, and mitochondrial m.1555A?>?G to the etiology of the non-syndromic deafness population in south China was 32.0%. Conclusions Our study is the first genetic analysis of non-syndromic hearing impairment in south China, and revealed that a clear genetic etiology accounted for 32.0% of non-syndromic hearing cases in patients from these regions. The mutational spectrum of non-syndromic hearing impairment in the south Chinese population provides useful and targeted information to aid in genetic counseling.

2014-01-01

277

Dissection of additive genetic variability for quantitative traits in chickens using SNP markers.  

PubMed

The aim of this study was to separate marked additive genetic variability for three quantitative traits in chickens into components associated with classes of minor allele frequency (MAF), individual chromosomes and marker density using the genomewide complex trait analysis (GCTA) approach. Data were from 1351 chickens measured for body weight (BW), ultrasound of breast muscle (BM) and hen house egg production (HHP), each bird with 354 364 SNP genotypes. Estimates of variance components show that SNPs on commercially available genotyping chips marked a large amount of genetic variability for all three traits. The estimated proportion of total variation tagged by all autosomal SNPs was 0.30 (SE 0.04) for BW, 0.33 (SE 0.04) for BM, and 0.19 (SE 0.05) for HHP. We found that a substantial proportion of this variation was explained by low frequency variants (MAF <0.20) for BW and BM, and variants with MAF 0.10-0.30 for HHP. The marked genetic variance explained by each chromosome was linearly related to its length (R(2)  = 0.60) for BW and BM. However, for HHP, there was no linear relationship between estimates of variance and length of the chromosome (R(2)  = 0.01). Our results suggest that the contribution of SNPs to marked additive genetic variability is dependent on the allele frequency spectrum. For the sample of birds analysed, it was found that increasing marker density beyond 100K SNPs did not capture additional additive genetic variance. PMID:24460953

Abdollahi-Arpanahi, R; Pakdel, A; Nejati-Javaremi, A; Moradi Shahrbabak, M; Morota, G; Valente, B D; Kranis, A; Rosa, G J M; Gianola, D

2014-06-01

278

A search for genetic markers associated with egg production in the ostrich (Struthio camelus).  

PubMed

The aim of the current study was to search for genetic markers, microsatellite loci associated with laying performance in ostriches. The material consisted of two groups of ostrich hens characterized by high or low laying performance (over 75 and less than 25 eggs per season, respectively). The investigation covered 30 microsatellite loci characteristic for the ostrich (the CAU group) and led to identification of significant differences in allele and genotype frequencies between the two groups of hens considered. Out of a total of 30 microsatellite loci examined, 28 showed different alleles in relation to analyzed performance groups. In hens of high laying performance (HP group, n = 12), specific alleles occurred in 23 microsatellite loci (40 alleles of 243 identified), while in those of low egg production (LP group, n = 12), they occurred in 22 (51 alleles of 243 identified). The results indicate the usefulness of the microsatellite loci as the potential genetic markers associated with laying performance that can be applied for genetic improvement of ostrich flocks. PMID:22544574

Kawka, M; Horba?czuk, J O; Jaszczak, K; Pierzcha?a, M; Cooper, R G

2012-08-01

279

Assessment of Genetic Diversity of Bermudagrass (Cynodon dactylon) Using ISSR Markers.  

PubMed

Bermudagrass (Cynodon spp.) is a major turfgrass for home lawns, public parks, golf courses and sport fields and is known to have originated in the Middle East. Morphological and physiological characteristics are not sufficient to differentiate some bermudagrass genotypes because the differences between them are often subtle and subjected to environmental influences. In this study, twenty seven bermudagrass accessions and introductions, mostly from different parts of Iran, were assayed by inter-simple sequence repeat (ISSR) markers to differentiate and explore their genetic relationships. Fourteen ISSR primers amplified 389 fragments of which 313 (80.5%) were polymorphic. The average polymorphism information content (PIC) was 0.328, which shows that the majority of primers are informative. Cluster analysis using the un-weighted paired group method with arithmetic average (UPGMA) method and Jaccard's similarity coefficient (r = 0.828) grouped the accessions into six main clusters according to some degree to geographical origin, their chromosome number and some morphological characteristics. It can be concluded that there exists a wide genetic base of bermudograss in Iran and that ISSR markers are effective in determining genetic diversity and relationships among them. PMID:22312259

Farsani, Tayebeh Mohammadi; Etemadi, Nematollah; Sayed-Tabatabaei, Badraldin Ebrahim; Talebi, Majid

2012-01-01

280

Microsatellite DNA markers indicate three genetic lineages in East Asian indigenous goat populations.  

PubMed

The genetic differentiation and phylogenetic relationships of 18 indigenous goat populations from seven East Asian countries were analysed based on data obtained from 26 microsatellite DNA markers. The mean number of alleles (MNA) per population ranged from 2.5 to 7.6, with an average of 5.8. Genetic variability estimated from MNA and heterozygosity (H(E) and H(O) ) were relatively low in coastal and island populations. A heterozygous deficiency within populations (F(IS) = 0.054, P < 0.001) and total inbreeding (F(IT) = 0.181, P < 0.01) were observed, and genetic differentiation in the populations (F(ST) ) was 13.4%. The results of Bayesian model-based clustering and a neighbour-joining tree based on Nei's genetic distance showed that Asian goat populations could be subdivided into at least the following three genetic clusters: East Asian, Southeast Asian and Mongolian. These results are in close accordance with conventional morphological and geographical classifications and migration history. PMID:22497600

Nomura, K; Ishii, K; Dadi, H; Takahashi, Y; Minezawa, M; Cho, C Y; Sutopo; Faruque, M O; Nyamsamba, D; Amano, T

2012-12-01

281

Genetic Diversity Analysis of Sugarcane Parents in Chinese Breeding Programmes Using gSSR Markers  

PubMed Central

Sugarcane is the most important sugar and bioenergy crop in the world. The selection and combination of parents for crossing rely on an understanding of their genetic structures and molecular diversity. In the present study, 115 sugarcane genotypes used for parental crossing were genotyped based on five genomic simple sequence repeat marker (gSSR) loci and 88 polymorphic alleles of loci (100%) as detected by capillary electrophoresis. The values of genetic diversity parameters across the populations indicate that the genetic variation intrapopulation (90.5%) was much larger than that of interpopulation (9.5%). Cluster analysis revealed that there were three groups termed as groups I, II, and III within the 115 genotypes. The genotypes released by each breeding programme showed closer genetic relationships, except the YC series released by Hainan sugarcane breeding station. Using principle component analysis (PCA), the first and second principal components accounted for a cumulative 76% of the total variances, in which 43% were for common parents and 33% were for new parents, respectively. The knowledge obtained in this study should be useful to future breeding programs for increasing genetic diversity of sugarcane varieties and cultivars to meet the demand of sugarcane cultivation for sugar and bioenergy use.

You, Qian; Xu, Liping; Zheng, Yifeng; Que, Youxiong

2013-01-01

282

Extensive Genetic Diversity, Unique Population Structure and Evidence of Genetic Exchange in the Sexually Transmitted Parasite Trichomonas vaginalis  

Microsoft Academic Search

BackgroundTrichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the

Melissa D. Conrad; Andrew W. Gorman; Julia A. Schillinger; Pier Luigi Fiori; Rossana Arroyo; Nancy Malla; Mohan Lal Dubey; Jorge Gonzalez; Susan Blank; William E. Secor; Jane M. Carlton

2012-01-01

283

Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar  

PubMed Central

Background The genus Nelumbo Adans. comprises two living species, N. nucifera Gaertan. (Asian lotus) and N. lutea Pers. (American lotus). A genetic linkage map is an essential resource for plant genetic studies and crop improvement but has not been generated for Nelumbo. We aimed to develop genomic simple sequence repeat (SSR) markers from the genome sequence and construct two genetic maps for Nelumbo to assist genome assembly and integration of a genetic map with the genome sequence. Results A total of 86,089 SSR motifs were identified from the genome sequences. Di- and tri-nucleotide repeat motifs were the most abundant, and accounted for 60.73% and 31.66% of all SSRs, respectively. AG/GA repeats constituted 51.17% of dinucleotide repeat motifs, followed by AT/TA (44.29%). Of 500 SSR primers tested, 386 (77.20%) produced scorable alleles with an average of 2.59 per primer, and 185 (37.00%) showed polymorphism among two parental genotypes, N. nucifera ‘Chinese Antique’ and N. lutea ‘AL1’, and six progenies of their F1 population. The normally segregating markers, which comprised 268 newly developed SSRs, 37 previously published SSRs and 53 sequence-related amplified polymorphism markers, were used for genetic map construction. The map for Asian lotus was 365.67 cM with 47 markers distributed in seven linkage groups. The map for American lotus was 524.51 cM, and contained 177 markers distributed in 11 genetic linkage groups. The number of markers per linkage group ranged from three to 34 with an average genetic distance of 3.97 cM between adjacent markers. Moreover, 171 SSR markers contained in linkage groups were anchored to 97 genomic DNA sequence contigs of ‘Chinese Antique’. The 97 contigs were merged into 60 scaffolds. Conclusion Genetic mapping of SSR markers derived from sequenced contigs in Nelumbo enabled the associated contigs to be anchored in the linkage map and facilitated assembly of the genome sequences of ‘Chinese Antique’. The present study reports the first construction of genetic linkage maps for Nelumbo, which can serve as reference linkage maps to accelerate characterization germplasm, genetic mapping for traits of economic interest, and molecular breeding with marker-assisted selection.

2012-01-01

284

Genetic structure and affinities among tribal populations of southern India: a study of 24 autosomal DNA markers  

Microsoft Academic Search

Summary We describe the genetic structure and affinities of five Dravidian-speaking tribal populations inhabiting the Nilgiri hills of Tamil Nadu, in south India, using 24 autosomal DNA markers. Our goals were: (i) to examine what evolutionary forces have most significantly impacted south Indian tribal genetic variation, and (ii) to test whether the phenotypic similarities of some south Indian tribal groups

H. Vishwanathan; E. Deepa; R. Cordaux; M. Stoneking; M. V. Usha Rani; P. P. Majumder

2004-01-01

285

Genetic diversity and population structure of an endangered Orchid ( Dendrobium loddigesii Rolfe) from China revealed by SRAP markers  

Microsoft Academic Search

Dendrobium loddigesii Rolfe is an endangered perennial herb with ornamental and medicinal value. Due to habitat deterioration and human over-exploitation, it has suffered a significant decline in abundance. Determining the level of genetic diversity and pattern of population genetic structure of this species would be helpful for its conservation and management. In this paper, sequence-related amplified polymorphism (SRAP) markers were

Xiaoyan Cai; Zhenyu Feng; Xiaoxiao Zhang; Wen Xu; Beiwei Hou; Xiaoyu Ding

2011-01-01

286

A DArT marker genetic map of perennial ryegrass (Lolium perenne L.) integrated with detailed comparative mapping information; comparison with existing DArT marker genetic maps of Lolium perenne, L. multiflorum and Festuca pratensis  

PubMed Central

Background Ryegrasses and fescues (genera, Lolium and Festuca) are species of forage and turf grasses which are used widely in agricultural and amenity situations. They are classified within the sub-family Pooideae and so are closely related to Brachypodium distachyon, wheat, barley, rye and oats. Recently, a DArT array has been developed which can be used in generating marker and mapping information for ryegrasses and fescues. This represents a potential common marker set for ryegrass and fescue researchers which can be linked through to comparative genomic information for the grasses. Results A F2 perennial ryegrass genetic map was developed consisting of 7 linkage groups defined by 1316 markers and deriving a total map length of 683 cM. The marker set included 866 DArT and 315 gene sequence-based markers. Comparison with previous DArT mapping studies in perennial and Italian ryegrass (L. multiflorum) identified 87 and 105 DArT markers in common, respectively, of which 94% and 87% mapped to homoeologous linkage groups. A similar comparison with meadow fescue (F. pratensis) identified only 28 DArT markers in common, of which c. 50% mapped to non-homoelogous linkage groups. In L. perenne, the genetic distance spanned by the DArT markers encompassed the majority of the regions that could be described in terms of comparative genomic relationships with rice, Brachypodium distachyon, and Sorghum bicolor. Conclusions DArT markers are likely to be a useful common marker resource for ryegrasses and fescues, though the success in aligning different populations through the mapping of common markers will be influenced by degrees of population interrelatedness. The detailed mapping of DArT and gene-based markers in this study potentially allows comparative relationships to be derived in future mapping populations characterised using solely DArT markers.

2013-01-01

287

Assessment of genetic markers for species differentiation within the Mycobacterium tuberculosis complex.  

PubMed Central

It is important to correctly identify species within the Mycobacterium tuberculosis complex because of the zoonotic implications of bovine tuberculosis, especially in developing countries. We assessed the use of various genetic markers for species-specific identification of mycobacteria from the M. tuberculosis complex. A multiplex PCR designed for detection of the mtp40 and IS1081 elements was optimized and evaluated in 339 mycobacterial strains from different animal and geographic origins. The host range of the IS6110, MPB70, and 16S rRNA genes was also studied by PCR in all the strains. Finally, the usefulness of the genetic markers was compared by an immunoperoxidase test for specific identification of Mycobacterium bovis strains. The mtp40 sequence was detected in 87 of the 91 strains of M. tuberculosis and in 9 of the 11 Mycobacterium africanum strains but not in any of the M. bovis or Mycobacterium microti strains, indicating that the mtp40 element was also found in all of the M. tuberculosis complex strains isolated from seals. This organism is considered to be a true seal pathogen, but its origin is essentially unknown. The finding of the mtp40 element in the strains from seals suggests a closer relationship of these strains with a human origin than to an animal origin. The mtp40 element was not found in any other mycobacterial species included in the study. As a result of this study, we suggest that biochemical tests or alternate genetic markers are still needed to differentiate M. tuberculosis from M. africanum when these species coexist as causative agents of tuberculosis. The immunoperoxidase test worked well for the identification of M. bovis strains. We also report, for the first time, PCR amplification of the repetitive element IS6110 in an isolate of Mycobacterium ulcerans and an isolate of Mycobacterium gilvum, which emphasizes the need for further investigation of the host range of this sequence.

Liebana, E; Aranaz, A; Francis, B; Cousins, D

1996-01-01

288

Using SSR markers to determine the population genetic structure of wild apricot ( Prunus armeniaca L.) in the Ily Valley of West China  

Microsoft Academic Search

Genetic structure of three wild populations (Xinyuan, Gongliu and Daxigou) of apricot in the Ily Valley, Xinjiang Uygur Autonomous Region of China, was investigated with microsatellite (simple sequence repeat, SSR) markers. The higher polymorphism and greater transportability of these markers between Prunus species proved SSR markers were much efficient for conducting genetic diversity studies in wild apricot. Nei’s gene diversity

He Tian-Ming; Chen Xue-Sen; Xu Zheng; Gao Jiang-Sheng; Lin Pei-Jun; Liu Wen; Liang Qing; Wu Yan

2007-01-01

289

Population genetics of the yellow fever mosquito in Trinidad: comparisons of amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers  

Microsoft Academic Search

Recent development of DNA markers provides powerful tools for population genetic analyses. Amplified fragment length polymorphism (AFLP) markers result from a poly- merase chain reaction (PCR)-based DNA fingerprinting technique that can detect multiple restriction fragments in a single polyacrylamide gel, and thus are potentially useful for population genetic studies. Because AFLP markers have to be analysed as dominant loci in

G. Yan; J. Romero-Severson; M. Walton; D. D. CHADEEand; D. W. Severson

1999-01-01

290

Genetic profiling of Bolivian population using 15 STR markers of forensic importance.  

PubMed

Allele frequencies for the 13 CODIS markers plus D2S1358 and D19S433 loci were estimated in a sample of 148 unrelated individuals from Bolivia and parameters of forensic interest were calculated. Further, the STR data were analyzed using a distance-based method to assess the genetic relationships of this population with other ones living in Argentina, Brazil, Costa Rica, Mexico, Peru, Venezuela and three autochthonous populations living in the Beni Department of Bolivia (Quechua, Aymara and Beni population). PMID:19285898

Riccardi, Laura Natalia; Melean, German; Rada, Ana; Tirado, Noemi; Genuardi, Maurizio; Ricci, Ugo

2009-05-01

291

Genetic characterization of 12 heterologous microsatellite markers for the giant tropical tree Cariniana legalis (Lecythidaceae)  

PubMed Central

Twelve microsatellite loci previously developed in the tropical tree Cariniana estrellensis were genetically characterized in Cariniana legalis. Polymorphisms were assessed in 28 C. legalis individuals found between the Pardo and Mogi-Guaçu River basins in the state of São Paulo, Brazil. Of the 12 loci, 10 were polymorphic and exhibited Mendelian inheritance. The allelic richness at each locus ranged from 2-11, with an average of 7 alleles per locus, and the expected heterozygosity ranged from 0.07-0.88. These loci showed a high probability of paternity exclusion. The characteristics of these heterologous microsatellite markers indicate that they are suitable tools for investigating questions concerning population genetics in C. legalis.

2010-01-01

292

Genetic diversity of Tomistoma schlegelii inferred from mtDNA markers.  

PubMed

The genetic diversity of the endangered crocodile Tomistoma schlegelii was characterized using the protein coding ND 6-tRNA(glu)-cyt b and the cytochrome b-control region (cyt b-CR) markers. Concatenate data revealed six haplotypes with an overall haplotype diversity of 0.769 ± 0.039; nucleotide diversity was 0.00535 ± 0.00172. A nearest-neighbor analysis showed that all individuals clustered with four geographic regions (Sumatra, Peninsular Malaysia, Sarawak, and East Kalimantan) and were genetically differentiated. With the exception of the individuals from haplotype H2, which occurred in both Peninsular Malaysia and Sarawak, all other haplotypes were geographically distinct. The H4 lineage, which was found to be the most divergent, clustered exclusively in the basal clade in all phylogenetic trees, and the haplotype network was unconnected at the 95% reconnection limit, suggesting further investigation to establish its possible status as a distinct evolutionary significant unit or a cryptic species. PMID:23325482

Kaur, Taranjeet; Japning, Jeffrine Rovie Ryan; Sabki, Mohamad Shahbudin; Sidik, Irvan; Chong, Lee Kim; Ong, Alan H K

2013-04-01

293

Is there a genetic contribution to cultural differences? Collectivism, individualism and genetic markers of social sensitivity  

PubMed Central

Genes and culture are often thought of as opposite ends of the nature–nurture spectrum, but here we examine possible interactions. Genetic association studies suggest that variation within the genes of central neurotransmitter systems, particularly the serotonin (5-HTTLPR, MAOA-uVNTR) and opioid (OPRM1 A118G), are associated with individual differences in social sensitivity, which reflects the degree of emotional responsivity to social events and experiences. Here, we review recent work that has demonstrated a robust cross-national correlation between the relative frequency of variants in these genes and the relative degree of individualism–collectivism in each population, suggesting that collectivism may have developed and persisted in populations with a high proportion of putative social sensitivity alleles because it was more compatible with such groups. Consistent with this notion, there was a correlation between the relative proportion of these alleles and lifetime prevalence of major depression across nations. The relationship between allele frequency and depression was partially mediated by individualism–collectivism, suggesting that reduced levels of depression in populations with a high proportion of social sensitivity alleles is due to greater collectivism. These results indicate that genetic variation may interact with ecological and social factors to influence psychocultural differences.

Lieberman, Matthew D.

2010-01-01

294

Is there a genetic contribution to cultural differences? Collectivism, individualism and genetic markers of social sensitivity.  

PubMed

Genes and culture are often thought of as opposite ends of the nature-nurture spectrum, but here we examine possible interactions. Genetic association studies suggest that variation within the genes of central neurotransmitter systems, particularly the serotonin (5-HTTLPR, MAOA-uVNTR) and opioid (OPRM1 A118G), are associated with individual differences in social sensitivity, which reflects the degree of emotional responsivity to social events and experiences. Here, we review recent work that has demonstrated a robust cross-national correlation between the relative frequency of variants in these genes and the relative degree of individualism-collectivism in each population, suggesting that collectivism may have developed and persisted in populations with a high proportion of putative social sensitivity alleles because it was more compatible with such groups. Consistent with this notion, there was a correlation between the relative proportion of these alleles and lifetime prevalence of major depression across nations. The relationship between allele frequency and depression was partially mediated by individualism-collectivism, suggesting that reduced levels of depression in populations with a high proportion of social sensitivity alleles is due to greater collectivism. These results indicate that genetic variation may interact with ecological and social factors to influence psychocultural differences. PMID:20592043

Way, Baldwin M; Lieberman, Matthew D

2010-06-01

295

Predicting risk in space: Genetic markers for differential vulnerability to sleep restriction  

NASA Astrophysics Data System (ADS)

Several laboratories have found large, highly reliable individual differences in the magnitude of cognitive performance, fatigue and sleepiness, and sleep homeostatic vulnerability to acute total sleep deprivation and to chronic sleep restriction in healthy adults. Such individual differences in neurobehavioral performance are also observed in space flight as a result of sleep loss. The reasons for these stable phenotypic differential vulnerabilities are unknown: such differences are not yet accounted for by demographic factors, IQ or sleep need, and moreover, psychometric scales do not predict those individuals cognitively vulnerable to sleep loss. The stable, trait-like (phenotypic) inter-individual differences observed in response to sleep loss—with intraclass correlation coefficients accounting for 58-92% of the variance in neurobehavioral measures—point to an underlying genetic component. To this end, we utilized multi-day highly controlled laboratory studies to investigate the role of various common candidate gene variants—each independently—in relation to cumulative neurobehavioral and sleep homeostatic responses to sleep restriction. These data suggest that common genetic variations (polymorphisms) involved in sleep-wake, circadian, and cognitive regulation may serve as markers for prediction of inter-individual differences in sleep homeostatic and neurobehavioral vulnerability to sleep restriction in healthy adults. Identification of genetic predictors of differential vulnerability to sleep restriction—as determined from candidate gene studies—will help identify astronauts most in need of fatigue countermeasures in space flight and inform medical standards for obtaining adequate sleep in space. This review summarizes individual differences in neurobehavioral vulnerability to sleep deprivation and ongoing genetic efforts to identify markers of such differences.

Goel, Namni; Dinges, David F.

2012-08-01

296

Genetic diversity of Palestine landraces of faba bean (Vicia faba) based on RAPD markers.  

PubMed

Until now, neither phenotypic nor molecular approaches have been used to characterize the landraces of Palestine faba beans (Vicia faba). We used PCR-based RAPD markers to determine the genetic diversity and relatedness among 26 Palestinian faba bean landraces (traditional farmers' varieties) from 8 localities in the West Bank, Palestine. In tests with 37 primers, 14 generated no polymorphic bands, 12 exhibited weak and unclear products, and 11 primers produced good amplification products with high intensity and pattern stability. Ninety-four DNA fragments (loci) were detected, with an average of 8.54 loci per primer and size ranging from 160 to 1370 bp. A minimum of 4 and a maximum of 14 DNA fragments were obtained using (OPA-05 and OPA-09) and (BC-261) primers, respectively. The maximum percentage of polymorphic markers was 71.4 (BC-298) and the minimum was 50.0 (OPA-05, -09, -16). The 11 primers exhibited relatively high collective resolving power (Rp) values of 26.316, and varied from 0.154 for the OPA-09 primer to 5.236 for the BC-261, with an overall mean of 2.392. The primers BC-261, -322, and -298 were found to be the most useful RAPD primers to assess the genetic diversity of Palestinian faba beans, as they revealed relatively high Rp rates (5.236, 3.618, and 3.150, respectively). Based on the Jaccard coefficient, the genetic distance ranged from 0.358 to 0.069, with a mean of 0.213. We conclude that the RAPD technique is useful for determining genetic diversity and for developing suitable fingerprints for faba bean landraces grown in Palestine. PMID:24065673

Basheer-Salimia, R; Shtaya, M; Awad, M; Abdallah, J; Hamdan, Y

2013-01-01

297

Genetic diversity and relationship of global faba bean (Vicia faba L.) germplasm revealed by ISSR markers.  

PubMed

Genetic diversity and relationships of 802 faba bean (Vicia faba L.) landraces and varieties from different geographical locations of China and abroad were examined using ISSR markers. A total of 212 repeatable amplified bands were generated with 11 ISSR primers, of which 209 were polymorphic. Accessions from North China showed highest genetic diversity, while accessions from central China showed low level of diversity. Chinese spring faba bean germplasm was clearly separated from Chinese winter faba bean, based on principal component analysis and UPGMA clustering analysis. Winter accessions from Zhejiang (East China), Jiangxi (East China), Sichuan (Southwest China) and Guizhou (Southwest China) were quite distinct to that from other provinces in China. Great differentiation between Chinese accessions and those from rest of the world was shown with a UPGMA dendrogram. AMOVA analyses demonstrated large variation and differentiation within and among groups of accessions from China. As a continental geographic group, accessions from Europe were genetically closer to those from North Africa. Based on ISSR data, grouping results of accessions from Asia, Europe and Africa were obviously associated with their geographical origin. The overall results indicated that the genetic relationship of faba bean germplasm was closely associated with their geographical origin and their ecological habit. PMID:22204023

Wang, Hai-Fei; Zong, Xu-Xiao; Guan, Jian-Ping; Yang, Tao; Sun, Xue-Lian; Ma, Yu; Redden, Robert

2012-03-01

298

Association of Genetic Markers with CSF Oligoclonal Bands in Multiple Sclerosis Patients  

PubMed Central

Objective to explore the association between genetic markers and Oligoclonal Bands (OCB) in the Cerebro Spinal Fluid (CSF) of Italian Multiple Sclerosis patients. Methods We genotyped 1115 Italian patients for HLA-DRB1*15 and HLA-A*02. In a subset of 925 patients we tested association with 52 non-HLA SNPs associated with MS susceptibility and we calculated a weighted Genetic Risk Score. Finally, we performed a Genome Wide Association Study (GWAS) with OCB status on a subset of 562 patients. The best associated SNPs of the Italian GWAS were replicated in silico in Scandinavian and Belgian populations, and meta-analyzed. Results HLA-DRB1*15 is associated with OCB+: p?=?0.03, Odds Ratio (OR)?=?1.6, 95% Confidence Limits (CL)?=?1.1–2.4. None of the 52 non-HLA MS susceptibility loci was associated with OCB, except one SNP (rs2546890) near IL12B gene (OR: 1.45; 1.09–1.92). The weighted Genetic Risk Score mean was significantly (p?=?0.0008) higher in OCB+ (7.668) than in OCB? (7.412) patients. After meta-analysis on the three datasets (Italian, Scandinavian and Belgian) for the best associated signals resulted from the Italian GWAS, the strongest signal was a SNP (rs9320598) on chromosome 6q (p?=?9.4×10?7) outside the HLA region (65 Mb). Discussion genetic factors predispose to the development of OCB.

Esposito, Federica; Lucenti, Ausiliatrice; Harbo, Hanne F.; Goris, An; Kockum, Ingrid; Oturai, Annette Bang; Celius, Elisabeth Gulowsen; Mero, Inger L.; Dubois, Benedicte; Olsson, Tomas; S?ndergaard, Helle Bach; Cusi, Daniele; Lupoli, Sara; Andreassen, Bettina Kulle; Myhr, Kjell-Morten; Guerini, Franca R.; Comi, Giancarlo

2013-01-01

299

Study Of Genetic Diversity Between Grasspea Landraces Using Morphological And Molecular Marker  

NASA Astrophysics Data System (ADS)

Grass pea is a beneficial crop to Iran since it has some major advantageous such as high grain and forage quality, high drought tolerance and medium level of salinity tolerance and a good native germplasm variation which accessible for breeding programs. This study was carried out to evaluate morphological traits of the grass pea landraces using a randomized complete block design with 3 replications at Research Farm of Isfahan University of Technology. To evaluate genetic diversity of 14 grass pea landraces from various locations in Iran were investigated using 32 RAPD & ISJ primers at Biocenter of University of Zabol. Analysis of variance indicated a highly significant differences among 14 grass pea landrace for the morphological traits. Average of polymorphism percentage of RAPD primer was 73.9%. Among used primer, 12 random primers showed polymorphism and a total of 56 different bands were observed in the genotypes. Jafar-abad and Sar-chahan genotypes with similarity coefficient of 66% and Khoram-abad 2 and Khoram-abad 7 genotypes with similarity coefficient of 3% were the most related and the most distinct genotypes, respectively. Fourteen primers out of 17 semi random primers produced 70 polymorphic bands which included 56% of the total 126 produced bands. Genetic relatedness among population was investigated using Jacard coefficient and unweighted pair group mean analysis (UPGMA) algorithm. The result of this research verified possibility of use of RAPD & ISJ markers for estimation of genetic diversity, management of genetic resources and determination of repetitive accessions in grass pea.

Sedehi, Abbasali Vahabi; Lotfi, Asefeh; Solooki, Mahmood

2008-01-01

300

Assessment of genetic diversity and conservation priority of Omani local chickens using microsatellite markers.  

PubMed

Designing strategies for conservation and improvement livestock should be based on assessment of genetic characteristics of populations under consideration. In Oman, conservation programs for local livestock breeds have been started. The current study assessed the genetic diversity and conservation potential of local chickens from Oman. Twenty-nine microsatellite markers were analyzed in 158 birds from six agro-ecological zones: Batinah, Dhofar, North Hajar, East Hajar, Musandam, and East Coast. Overall, a total of 217 alleles were observed. Across populations, the average number of alleles per locus was 7.48 and ranged from 2 (MCW98 and MCW103) to 20 (LEI094). The mean expected heterozygosity (H E) was 0.62. Average fixation index among populations (F ST) was 0.034, indicating low population differentiation, while the mean global deficit of heterozygotes across populations (F IT) was 0.159. Based on Nei's genetic distance, a neighbor-joining tree was constructed for the populations, which clearly identified the Dhofar population as the most distant one of the Omani chicken populations. The analysis of conservation priorities identified Dhofar and Musandam populations as the ones that largely contribute to the maximal genetic diversity of the Omani chicken gene pool. PMID:24590534

Al-Qamashoui, Badar; Simianer, Henner; Kadim, Isam; Weigend, Steffen

2014-06-01

301

Genetic variability in spotted seatrout (Cynoscion nebulosus), determined with microsatellite DNA markers  

USGS Publications Warehouse

Variation in the allele frequencies of five microsatellite loci was surveyed in 1256 individual spotted seatrout (Cynoscion nebulosus) obtained from 12 bays and estuaries from Laguna Madre, Texas, to Charlotte Harbor, Florida, to St. John's River on the Florida Atlantic Coast. Texas and Louisiana collection sites were resampled each year for two to four years (1998-2001). Genetic differentiation was observed. Spotted seatrout from Florida waters were strongly differentiated from spotted seatrout collected in Louisiana and Texas. The greatest genetic discontinuity was observed between Tampa Bay and Charlotte Harbor, and Charlotte Harbor seatrout were most similar to Atlantic Coast spotted seatrout. Texas and Louisiana samples were not strongly structured within the northwestern Gulf of Mexico and there was little evidence of temporal differentiation within bays. These findings are contrary to those of earlier analyses with allozymes and mitochondrial DNA (mtDNA) where evidence of spatial differentiation was found for spotted seatrout resident on the Texas coast. The differences in genetic structure observed among these markers may reflect differences in response to selective pressure, or may be due to differences in underlying genetic processes.

Ward, R.; Bowers, K.; Hensley, R.; Mobley, B.; Belouski, E.

2007-01-01

302

Analysis of genetic variability and population structure of the endemic medicinal Limonium sinense using molecular markers.  

PubMed

Limonium sinense is an endemic medicinal herb used to treat fever, hemorrhage and other disorders. In the present study, population genetic diversity was elucidated using random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) primers. Percentage of polymorphic bands, Nei's gene diversity and Shannon's information index revealed a high level of genetic diversity at species level. The analysis of molecular variance revealed that 69.88% (RAPD), 71.19% (ISSR) and 70.97% (AFLP) of variability were partitioned among individuals within populations, which indicated the coherent trend by Gst (0.3849/0.3577/0.3670). Gene flow number (Nm) was 0.581/0.618/0.612, which indicated that there was a limited gene exchange between populations. The UPGMA clustering results showed that the genetic distance had no significant correlation with geographic distance. These results indicate that these markers were reliable tools for the differentiation and determination of the genetic diversity among the populations of L. sinense and the conservation of existing natural population is necessary. PMID:23506829

Ding, Ge; Zhang, Daizhen; Yu, Yanqiu; Zhao, Lingling; Zhang, Beibei

2013-05-15

303

Analysis of genetic stability of in vitro propagated potato microtubers using DNA markers.  

PubMed

The genetic stability of in vitro propagated potato microtubers was assessed using random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR), simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers. Microtubers were developed through in vitro from potato microplants using standardized protocols. The microtubers were conserved for 1 year under three different culture media and consequently microplants were regenerated for the DNA analyses. During the study, a total of 38 (10 RAPD, 11 ISSR, 12 SSR and 5 AFLP) primers produced a total of 407 (58 RAPD, 56 ISSR, 96 SSR and 197 AFLP) clear, distinct and reproducible amplicons. Cluster analysis revealed 100 % genetic similarity among the mother plant and its derivatives within the clusters by SSR, ISSR and RAPD analyses, whereas AFLP analysis revealed from 85 to 100 % genetic similarity. Dendrogram analysis based on the Jaccard's coefficient classified the genotypes into five clusters (I-V), each cluster consisting of mother plant and its derivatives. Principal component analysis (PCA) also plotted mother plant and its genotypes of each cluster together. Based on our results, it is concluded that AFLP is the best method followed by SSR, ISSR and RAPD to detect genetic stability of in vitro conserved potato microtubers. The in vitro conservation medium (T2) is a safe method for conservation of potato microtubers to produce true-to-type plans. PMID:24431528

Tiwari, Jagesh K; Chandel, Poonam; Gupta, Shruti; Gopal, Jai; Singh, B P; Bhardwaj, Vinay

2013-10-01

304

Population genetics of Sargassum horneri (Fucales, Phaeophyta) in China revealed by ISSR and SRAP markers  

NASA Astrophysics Data System (ADS)

Sargassum horneri is a common brown macro-alga that is found in the inter-tidal ecosystems of China. To investigate the current status of seaweed resources and provide basic data for its sustainable development, ISSR (inter simple sequence repeat) and SRAP (sequence related amplified polymorphism) markers were used to analyze the population genetics among nine natural populations of S. horneri. The nine studied populations were distributed over 2 000 km from northeast to south China. The percentage of polymorphic loci P % (ISSR, 99.44%; SRAP, 100.00%), Nei's genetic diversity H (ISSR, 0.107-0.199; SRAP, 0.100-0.153), and Shannon's information index I (ISSR, 0.157-0.291; SRAP, 0.148-0.219) indicated a fair amount of genetic variability among the nine populations. Moreover, the high degree of gene differentiation G st (ISSR, 0.654; SRAP, 0.718) and low gene flow N m (ISSR, 0.265; SRAP, 0.196) implied that there was significant among-population differentiation, possibly as a result of habitat fragmentation. The matrices of genetic distances and fixation indices ( F st) among the populations correlated well with their geographical distribution (Mantel test R =0.541 5, 0.541 8; P =0.005 0, 0.002 0 and R =0.728 6, 0.641 2; P =0.001 0, 0.001 0, respectively); the Rongcheng population in the Shandong peninsula was the only exception. Overall, the genetic differentiation agreed with the geographic isolation. The fair amount of genetic diversity that was revealed in the S. horneri populations in China indicated that the seaweed resources had not been seriously affected by external factors.

Yu, Shenhui; Chong, Zhuo; Zhao, Fengjuan; Yao, Jianting; Duan, Delin

2013-05-01

305

Fingertips Ischemia, Nephroangiosclerosis, and Focal Segmental Glomerulosclerosis: Is Genetic Thrombophilia the Unique Explanation?  

PubMed Central

Case Presentation. 53-years-old-man with essential hypertension and nonnephrotic proteinuria (1.3?gr/24?h) and with normal renal function (eGFR-MDRD 123?mL/min/1.73?m2) was admitted to nephrology department; kidney biopsy showed FSGS; two years later the patient presented with ulceration and ischemic gangrene of the IV and V right-hand fingertips; genetic analysis demonstrated polymorphism of the methylenetetrahydrofolate reductase genes C677T (heterozygote C677T/1298AC with normal value of homocysteine) and mutations of prothrombin gene G20210A and of plasminogen activator inhibitor-1 4G/5G 675 with slight increase of its value. After five years from biopsy, 24-hours proteinuria was still around 1–1.3?g/die; renal function was still normal (eGFR 107?ml/min/1.73?m2). These data are against the previous diagnosis of primary FSGS. We hypothesize that genetic thrombophilia may explain all the clinical signs of our patient. Conclusions. Alterations in genes of thrombophilia should be ruled out in patients with bioptic diagnosis of “primary” FSGS, in particular if clinically atypical.

2014-01-01

306

Identification of genetic markers for fat deposition and meat tenderness on bovine chromosome 5: Development of a low-density single nucleotide polymorphism map1,2  

Microsoft Academic Search

As genetic markers, SNP are well suited for the development of genetic tests for produc- tion traits in livestock. They are stable through many generations and can provide direct assessment of indi- vidual animal's genetic merit if they are in linkage dis- equilibrium and phase with functional genetic varia- tion. Bovine chromosome 5 has been shown to harbor genetic variation

R. T. Stone; E. Casas; T. P. L. Smith; J. W. Keele; G. Harhay; G. L. Bennett; M. Koohmaraie; T. L. Wheeler; S. D. Shackelford; W. M. Snelling

307

A method for gene amplification and simultaneous deletion in Corynebacterium glutamicum genome without any genetic markers.  

PubMed

A method for the simultaneous replacement of a given gene by a target gene, leaving no genetic markers, has been developed. The method is based on insertional inactivation and double-crossover homologous recombination. With this method, the lysC(T311I), fbp and ddh genes were inserted into Corynebacterium glutamicum genome, and the pck, alaT and avtA genes were deleted. Mobilizable plasmids with lysC(T311I), fbp and ddh cassettes and two homologous arms on the ends of pck, alaT and avtA were constructed, and then transformed into C. glutamicum. The target-expression cassettes were inserted in the genome via the first homologous recombination, and the genetic markers were removed via the second recombination. The target-transformants were sequentially screened from kanamycin-resistance and sucrose-resistance plates. The enzyme activities of transformants were stably maintained for 30 generations under non-selective culture conditions, suggesting that the integrated cassettes in host were successfully expressed and maintained as stable chromosomal insertions in C. glutamicum. The target-transformants were used to optimize the l-lysine production, showing that the productions were strongly increased because the selected genes were closely linked to l-lysine production. In short, this method can be used to construct amino acid high-producing strains with unmarked gene amplification and simultaneous deletion in genome. PMID:24613758

Xu, Jianzhong; Xia, Xiuhua; Zhang, Junlan; Guo, Yanfeng; Qian, He; Zhang, Weiguo

2014-03-01

308

Population genetics and drug resistance markers: an essential for malaria surveillance in Pakistan.  

PubMed

Plasmodium (P.) vivax is the prevalent malarial species accounting for 70% of malaria cases in Pakistan. However, baseline epidemiological data on P. vivax population structure and drug resistance are lacking from Pakistan. For population structure studies, molecular genetic markers, circumsporozoite protein (csp) and merozoite surface protein-1 (msp-1) are considered useful as these play an important role in P. vivax survival under immune and environmental pressure. Furthermore, these genes have also been identified as suitable candidates for vaccine development. While efforts for effective vaccine are underway, anti-malarial agents remain the mainstay for control. Evidence of resistance against commonly used anti-malarial agents, particularly Sulphadoxine-Pyrimethamine (SP) is threatening to make this form of control defunct. Therefore, studies on drug resistance are necessary so that anti-malarial treatment strategies can be structured and implemented accordingly by the Malaria Control Program, Pakistan. This review aims to provide information on genetic markers of P. vivax population structure and drug resistance and comment on their usefulness in molecular surveillance and control. PMID:24304992

Raza, Afsheen; Beg, Mohammad Asim

2013-12-01

309

Performance assessment PCR-based assays targeting bacteroidales genetic markers of bovine fecal pollution.  

PubMed

There are numerous PCR-based assays available to characterize bovine fecal pollution in ambient waters. The determination of which approaches are most suitable for field applications can be difficult because each assay targets a different gene, in many cases from different microorganisms, leading to variation in assay performance. We describe a performance evaluation of seven end-point PCR and real-time quantitative PCR (qPCR) assays reported to be associated with either ruminant or bovine feces. Each assay was tested against a reference collection of DNA extracts from 247 individual bovine fecal samples representing 11 different populations and 175 fecal DNA extracts from 24 different animal species. Bovine-associated genetic markers were broadly distributed among individual bovine samples ranging from 39 to 93%. Specificity levels of the assays spanned 47.4% to 100%. End-point PCR sensitivity also varied between assays and among different bovine populations. For qPCR assays, the abundance of each host-associated genetic marker was measured within each bovine population and compared to results of a qPCR assay targeting 16S rRNA gene sequences from Bacteroidales. Experiments indicate large discrepancies in the performance of bovine-associated assays across different bovine populations. Variability in assay performance between host populations suggests that the use of bovine microbial source-tracking applications will require a priori characterization at each watershed of interest. PMID:20061457

Shanks, Orin C; White, Karen; Kelty, Catherine A; Hayes, Sam; Sivaganesan, Mano; Jenkins, Michael; Varma, Manju; Haugland, Richard A

2010-03-01

310

Genetic Variability in Markers of HLA-C Expression in Two Diverse South African Populations  

PubMed Central

An insertion-deletion (indel) polymorphism within the 3? untranslated region (UTR) of HLA-C has been shown to be involved in the regulation of HLA-C expression. Individuals who carry a deletion at this position exhibit increased HLA-C expression, which associates with lower viral set point in HIV-1 infected individuals. This 263 indel (rs67384697) is reported to be in strong linkage disequilibrium (LD) with a single nucleotide polymorphism (SNP) 35 kilobases upstream of HLA-C (-35T/C; rs9264942) in Caucasian individuals, making this SNP a potential marker for both HLA-C expression and HIV-1 disease progression. We therefore examined genetic variation within the HLA-C 3? UTR of 265 Black and Caucasian South Africans by direct sequencing and identified haplotypes encompassing the 263 indel and another indel at position 230 in both populations. Concomitant evaluation of variability at the ?35 SNP revealed this polymorphism to be an inappropriate marker for the 263 indel in these populations. These findings provide important insights into genetic variability within the regulatory regions of HLA-C that have potential implications for our understanding of the regulation of HLA-C expression and its impact on HIV-1 disease progression.

Gentle, Nikki L.; Paximadis, Maria; Puren, Adrian; Tiemessen, Caroline T.

2013-01-01

311

Performance Assessment PCR-Based Assays Targeting Bacteroidales Genetic Markers of Bovine Fecal Pollution?  

PubMed Central

There are numerous PCR-based assays available to characterize bovine fecal pollution in ambient waters. The determination of which approaches are most suitable for field applications can be difficult because each assay targets a different gene, in many cases from different microorganisms, leading to variation in assay performance. We describe a performance evaluation of seven end-point PCR and real-time quantitative PCR (qPCR) assays reported to be associated with either ruminant or bovine feces. Each assay was tested against a reference collection of DNA extracts from 247 individual bovine fecal samples representing 11 different populations and 175 fecal DNA extracts from 24 different animal species. Bovine-associated genetic markers were broadly distributed among individual bovine samples ranging from 39 to 93%. Specificity levels of the assays spanned 47.4% to 100%. End-point PCR sensitivity also varied between assays and among different bovine populations. For qPCR assays, the abundance of each host-associated genetic marker was measured within each bovine population and compared to results of a qPCR assay targeting 16S rRNA gene sequences from Bacteroidales. Experiments indicate large discrepancies in the performance of bovine-associated assays across different bovine populations. Variability in assay performance between host populations suggests that the use of bovine microbial source-tracking applications will require a priori characterization at each watershed of interest.

Shanks, Orin C.; White, Karen; Kelty, Catherine A.; Hayes, Sam; Sivaganesan, Mano; Jenkins, Michael; Varma, Manju; Haugland, Richard A.

2010-01-01

312

Meta-analyses between 18 candidate genetic markers and overweight/obesity  

PubMed Central

Aims The goal of our study is to investigate the associations between 18 candidate genetic markers and overweight/obesity. Methods A total of 72 eligible articles were retrieved from literature databases including PubMed, Embase, SpingerLink, Web of Science, Chinese National Knowledge Infrastructure (CNKI), and Wanfang. Meta-analyses of 18 genetic markers among 56,738 controls and 48,148 overweight/obese persons were done by Review Manager 5.0. Results Our results showed that SH2B1 rs7498665 polymorphism was significantly associated with the risk of overweight/obesity (overall odds ratio (OR)?=?1.21, 95% confidence interval (CI)?=?1.09-1.34, P?=?0.0004). Increased risk of overweight/obesity was also observed in FAIM2 rs7138803 polymorphism (overall OR?=?1.11, 95% CI?=?1.01-1.22, P?=?0.04). Conclusion Our meta-analyses have shown the important role of 2 polymorphisms (SH2B1 rs7498665 and FAIM2 rs7138803) in the development of overweight/obesity. This study highlighted the importance of above two candidate genes (SH2B1 and FAIM2) in the risk of overweight/obesity. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/2785487401176182.

2014-01-01

313

Genetic diversity and relatedness of sweet cherry (prunus avium L.) cultivars based on single nucleotide polymorphic markers.  

PubMed

Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD, and simple sequence repeat (SSR) markers. This study was carried out to assess the utility of single nucleotide polymorphism (SNP) markers generated from 3' untranslated regions (UTR) for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars, and old cultivars imported from different parts of the world were screened with seven SSR markers developed from other Prunus species and with 40 SNPs obtained from 3' UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity, and polymorphic information content values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, "Stella" was separated from "Compact Stella." This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3' UTR SNPs for genetic fingerprinting, parentage verification, gene mapping, and study of genetic diversity in sweet cherry. PMID:22737155

Fernandez I Marti, Angel; Athanson, Blessing; Koepke, Tyson; Font I Forcada, Carolina; Dhingra, Amit; Oraguzie, Nnadozie

2012-01-01

314

Genetic Diversity and Relatedness of Sweet Cherry (Prunus Avium L.) Cultivars Based on Single Nucleotide Polymorphic Markers  

PubMed Central

Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD, and simple sequence repeat (SSR) markers. This study was carried out to assess the utility of single nucleotide polymorphism (SNP) markers generated from 3? untranslated regions (UTR) for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars, and old cultivars imported from different parts of the world were screened with seven SSR markers developed from other Prunus species and with 40 SNPs obtained from 3? UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity, and polymorphic information content values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, “Stella” was separated from “Compact Stella.” This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3? UTR SNPs for genetic fingerprinting, parentage verification, gene mapping, and study of genetic diversity in sweet cherry.

Fernandez i Marti, Angel; Athanson, Blessing; Koepke, Tyson; Font i Forcada, Carolina; Dhingra, Amit; Oraguzie, Nnadozie

2012-01-01

315

Distribution of genetic markers of fecal pollution on a freshwater sandy shoreline in proximity to wastewater effluent.  

PubMed

Water, sand, and sediment from a Lake Superior harbor site continuously receiving wastewater effluent was sampled monthly for June to October 2010 and from May to September 2011. Understanding the dynamics of genetic markers of fecal bacteria in these matrices is essential to accurately characterizing health risks. Genetic markers for enterococci, total Bacteroides, and human-associated Bacteroides were measured in site-water, sand, and sediment and in final effluent by quantitative PCR. The similarity between the quantity of molecular markers in the water column and effluent indicated that the abundance of genetic markers in the water column was likely controlled by effluent inputs. Effluent turbidity was positively correlated (p ? 0.05) with AllBac and HF183 in final effluent and AllBac in the water column. In sand and sediment, Entero1 and AllBac were most abundant in the upper 1-3 cm depths, whereas HF183 was most abundant in the upper 1 cm of sand and at 7 cm in sediment. The AllBac and Entero1 markers were 1- and 2-orders of magnitude more abundant in sand and sediment relative to the water column per unit mass. These results indicate that sand and sediment may act as reservoirs for genetic markers of fecal pollution at some freshwater sites. PMID:23473470

Eichmiller, Jessica J; Hicks, Randall E; Sadowsky, Michael J

2013-04-01

316

Distribution of genetic markers of fecal pollution on a freshwater sandy shoreline in proximity to wastewater effluent  

PubMed Central

Water, sand, and sediment from a Lake Superior harbor site continuously receiving wastewater effluent was sampled monthly for June to October 2010 and from May to September 2011. Understanding the dynamics of genetic markers of fecal bacteria in these matrices is essential to accurately characterizing health risks. Genetic markers for enterococci, total Bacteroides, and human-associated Bacteroides were measured in site-water, sand, and sediment and in final effluent by quantitative PCR. The similarity between the quantity of molecular markers in the water column and effluent indicated that the abundance of genetic markers in the water column was likely controlled by effluent inputs. Effluent turbidity was positively correlated (p ? 0.05) with AllBac and HF183 in final effluent and AllBac in the water column. In sand and sediment, Entero1 and AllBac were most abundant in the upper 1– 3 cm depths, whereas HF183 was most abundant in the upper 1 cm of sand and at 7 cm in sediment. The AllBac and Entero1 markers were 1- and 2-orders of magnitude more abundant in sand and sediment relative to the water column per unit mass. These results indicate that sand and sediment may act as reservoirs for genetic markers of fecal pollution at some freshwater sites.

Eichmiller, Jessica J.; Hicks, Randall E.; Sadowsky, Michael J.

2013-01-01

317

Genetic linkage map of 46 DNA markers on human chromosome 16.  

PubMed Central

We have constructed a genetic linkage map of human chromosome 16 based on 46 DNA markers that detect restriction fragment length polymorphisms. Segregation data were collected on a set of multigenerational families provided by the Centre d'Etude du Polymorphisme Humain, and maps were constructed using recently developed multipoint analysis techniques. The map spans 115 centimorgans (cM) in males and 193 cM in females. Over much of the chromosome there is a significantly higher frequency of recombination in females than males. Near the alpha-globin locus on the distal part of the short arm, however, there is a significant excess of male recombination. Twenty-seven (59%) of the markers on the map have heterozygosities greater than or equal to 0.50. The largest interval between loci on the sex-average map is 14 cM and the average marker spacing is 3 cM. Using loci on this map, one could detect linkage to a dominant disease on chromosome 16 with as few as 10-15 phase-known meioses.

Keith, T P; Green, P; Reeders, S T; Brown, V A; Phipps, P; Bricker, A; Falls, K; Rediker, K S; Powers, J A; Hogan, C

1990-01-01

318

Characterization of a New Vaccinia virus Isolate Reveals the C23L Gene as a Putative Genetic Marker for Autochthonous Group 1 Brazilian Vaccinia virus  

PubMed Central

Since 1999, several Vaccinia virus (VACV) isolates, the etiological agents of bovine vaccinia (BV), have been frequently isolated and characterized with various biological and molecular methods. The results from these approaches have grouped these VACV isolates into two different clusters. This dichotomy has elicited debates surrounding the origin of the Brazilian VACV and its epidemiological significance. To ascertain vital information to settle these debates, we and other research groups have made efforts to identify molecular markers to discriminate VACV from other viruses of the genus Orthopoxvirus (OPV) and other VACV-BR groups. In this way, some genes have been identified as useful markers to discriminate between the VACV-BR groups. However, new markers are needed to infer ancestry and to correlate each sample or group with its unique epidemiological and biological features. The aims of this work were to characterize a new VACV isolate (VACV DMTV-2005) molecularly and biologically using conserved and non-conserved gene analyses for phylogenetic inference and to search for new genes that would elucidate the VACV-BR dichotomy. The VACV DMTV-2005 isolate reported in this study is biologically and phylogenetically clustered with other strains of Group 1 VACV-BR, the most prevalent VACV group that was isolated during the bovine vaccinia outbreaks in Brazil. Sequence analysis of C23L, the gene that encodes for the CC-chemokine-binding protein, revealed a ten-nucleotide deletion, which is a new Group 1 Brazilian VACV genetic marker. This deletion in the C23L open reading frame produces a premature stop-codon that is shared by all Group 1 VACV-BR strains and may also reflect the VACV-BR dichotomy; the deletion can also be considered to be a putative genetic marker for non-virulent Brazilian VACV isolates and may be used for the detection and molecular characterization of new isolates.

Oliveira, Danilo B.; Franco-Luiz, Ana P. M.; Campos, Rafael K.; Guedes, Maria I. M.; Fonseca, Flavio G.; Trindade, Giliane S.; Drumond, Betania P.; Kroon, Erna G.; Abrahao, Jonatas S.

2012-01-01

319

Estimating Additive and Non-Additive Genetic Variances and Predicting Genetic Merits Using Genome-Wide Dense Single Nucleotide Polymorphism Markers  

PubMed Central

Non-additive genetic variation is usually ignored when genome-wide markers are used to study the genetic architecture and genomic prediction of complex traits in human, wild life, model organisms or farm animals. However, non-additive genetic effects may have an important contribution to total genetic variation of complex traits. This study presented a genomic BLUP model including additive and non-additive genetic effects, in which additive and non-additive genetic relation matrices were constructed from information of genome-wide dense single nucleotide polymorphism (SNP) markers. In addition, this study for the first time proposed a method to construct dominance relationship matrix using SNP markers and demonstrated it in detail. The proposed model was implemented to investigate the amounts of additive genetic, dominance and epistatic variations, and assessed the accuracy and unbiasedness of genomic predictions for daily gain in pigs. In the analysis of daily gain, four linear models were used: 1) a simple additive genetic model (MA), 2) a model including both additive and additive by additive epistatic genetic effects (MAE), 3) a model including both additive and dominance genetic effects (MAD), and 4) a full model including all three genetic components (MAED). Estimates of narrow-sense heritability were 0.397, 0.373, 0.379 and 0.357 for models MA, MAE, MAD and MAED, respectively. Estimated dominance variance and additive by additive epistatic variance accounted for 5.6% and 9.5% of the total phenotypic variance, respectively. Based on model MAED, the estimate of broad-sense heritability was 0.506. Reliabilities of genomic predicted breeding values for the animals without performance records were 28.5%, 28.8%, 29.2% and 29.5% for models MA, MAE, MAD and MAED, respectively. In addition, models including non-additive genetic effects improved unbiasedness of genomic predictions.

Su, Guosheng; Christensen, Ole F.; Ostersen, Tage; Henryon, Mark; Lund, Mogens S.

2012-01-01

320

A High Density Consensus Genetic Map of Tetraploid Cotton That Integrates Multiple Component Maps through Molecular Marker Redundancy Check  

PubMed Central

A consensus genetic map of tetraploid cotton was constructed using six high-density maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cutoff. As a result, 20% of the markers (3,410) could be considered as redundant with some other markers. The marker redundancy information had been a crucial part of the map integration process, in which the six most informative interspecific Gossypium hirsutum×G. barbadense genetic maps were used for assembling a high density consensus (HDC) map for tetraploid cotton. With redundant markers being removed, the HDC map could be constructed thanks to the sufficient number of collinear non-redundant markers in common between the component maps. The HDC map consists of 8,254 loci, originating from 6,669 markers, and spans 4,070 cM, with an average of 2 loci per cM. The HDC map presents a high rate of locus duplications, as 1,292 markers among the 6,669 were mapped in more than one locus. Two thirds of the duplications are bridging homoeologous AT and DT chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per AT/DT chromosome pair. Sequences of 4,744 mapped markers were used for a mutual blast alignment (BBMH) with the 13 major scaffolds of the recently released Gossypium raimondii genome indicating high level of homology between the diploid D genome and the tetraploid cotton genetic map, with only a few minor possible structural rearrangements. Overall, the HDC map will serve as a valuable resource for trait QTL comparative mapping, map-based cloning of important genes, and better understanding of the genome structure and evolution of tetraploid cotton.

Blenda, Anna; Fang, David D.; Rami, Jean-Francois; Garsmeur, Olivier; Luo, Feng; Lacape, Jean-Marc

2012-01-01

321

Assessment of genetic diversity and relationships among Egyptian mango (Mangifera indica L.) cultivers grown in Suez Canal and Sinai region using RAPD markers.  

PubMed

DNA-based RAPD (Random Amplification of Polymorphic DNA) markers have been used extensively to study genetic diversity and relationships in a number of fruit crops. In this study, 10 (7 commercial mango cultivars and 3 accessions) mango genotypes traditionally grown in Suez Canal and Sinai region of Egypt, were selected to assess genetic diversity and relatedness. Total genomic DNA was extracted and subjected to RAPD analysis using 30 arbitrary 10-mer primers. Of these, eleven primers were selected which gave 92 clear and bright fragments. A total of 72 polymorphic RAPD bands were detected out of 92 bands, generating 78% polymorphisms. The mean PIC values scores for all loci were of 0.85. This reflects a high level of discriminatory power of a marker and most of these primers produced unique band pattern for each cultivar. A dendrogram based on Nei's Genetic distance co-efficient implied a moderate degree of genetic diversity among the cultivars used for experimentation, with some differences. The hybrid which had derived from cultivar as female parent was placed together. In the cluster, the cultivars and accessions formed separate groups according to bearing habit and type of embryo and the members in each group were very closely linked. Cluster analysis clearly showed two main groups, the first consisting of indigenous to the Delta of Egypt cultivars and the second consisting of indigenous to the Suez Canal and Sinai region. From the analysis of results, it appears the majority of mango cultivars originated from a local mango genepool and were domesticated later. The results indicated the potential of RAPD markers for the identification and management of mango germplasm for breeding purposes. PMID:24783778

Mansour, Hassan; Mekki, Laila E; Hussein, Mohammed A

2014-01-01

322

DNA-Based Genetic Markers for Rapid Cycling Brassica Rapa (Fast Plants Type) Designed for the Teaching Laboratory  

PubMed Central

We have developed DNA-based genetic markers for rapid cycling Brassica rapa (RCBr), also known as Fast Plants. Although markers for B. rapa already exist, ours were intentionally designed for use in a teaching laboratory environment. The qualities we selected for were robust amplification in PCR, polymorphism in RCBr strains, and alleles that can be easily resolved in simple agarose slab gels. We have developed two single nucleotide polymorphism (SNP) based markers and 14 variable number tandem repeat (VNTR)-type markers spread over four chromosomes. The DNA sequences of these markers represent variation in a wide range of genomic features. Among the VNTR-type markers, there are examples of variation in a non-genic region, variation within an intron, and variation in the coding sequence of a gene. Among the SNP-based markers there are examples of polymorphism in intronic DNA and synonymous substitution in a coding sequence. Thus these markers can serve laboratory exercises in both transmission genetics and molecular biology.

Slankster, Eryn E.; Chase, Jillian M.; Jones, Lauren A.; Wendell, Douglas L.

2012-01-01

323

Genetic diversity and identification of Chinese-grown pecan using ISSR and SSR markers.  

PubMed

Pecan is an important horticultural nut crop originally from North America and now widely cultivated in China for its high ecological, ornamental and economic value. Currently, there are over one hundred cultivars grown in China, including introduced American cultivars and Chinese seedling breeding cultivars. Molecular markers were used to assess the genetic diversity of these cultivars and to identify the pedigrees of fine pecan plants with good characteristics and no cultivar-related data. A total of 77 samples grown in China were studied, including 14 introduced cultivars, 12 domestic seedling breeding cultivars, and 49 fine pecan plants with no cultivar data, together with Carya cathayensis and Juglans nigra. A total of 77 ISSR and 19 SSR primers were prescreened; 10 ISSR and eight SSR primers were selected, yielding a total of 94 amplified bands (100% polymorphic) in the range of 140-1,950 bp for the ISSR and 70 amplified bands (100% polymorphic) in the range of 50-350 bp for SSR markers. Genetic diversity analyses indicated Chinese-grown pecan cultivars and fine plants had significant diversity at the DNA level. The dengrograms constructed with ISSR, SSR or combined data were very similar, but showed very weak grouping association with morphological characters. However, the progeny were always grouped with the parents. The great diversity found among the Chinese cultivars and the interesting germplasm of the fine pecan plants analyzed in this study are very useful for increasing the diversity of the pecan gene pool. All 77 accessions in this study could be separated based on the ISSR and SSR fingerprints produced by one or more primers. The results of our study also showed that ISSR and SSR techniques were both suitable for genetic diversity analyses and the identification of pecan resources. PMID:22146370

Jia, Xiao-Dong; Wang, Tao; Zhai, Min; Li, Yong-Rong; Guo, Zhong-Ren

2011-01-01

324

A multi-farm assessment of Greek black pig genetic diversity using microsatellite molecular markers.  

PubMed

Local breeds are important for the maintenance of genetic diversity and future food security. Nowadays, the worldwide distribution of pigs is dominated by a few breeds, tending towards a severe loss of pig biodiversity. Thus, it is critical to maintain distinct populations of pig breeds. The Greek black pig, a breed raised locally and known for the high quality of its meat for cured products, is the only traditional indigenous pig breed reared in Greece. We investigated the genetic diversity, based on microsatellite analysis, of the Greek black pig and evaluated its genetic uniqueness. One hundred and three pigs from 12 Greek farms were analyzed using 11 microsatellites. The total number of alleles amounted to 135, with a mean number of alleles per locus of 12.27, ranging between 10 and 16 alleles. The observed heterozygosity ranged from 0.363 to 0.825 per locus. The expected heterozygosity ranged from 0.471 to 0.707. The inbreeding coefficient ranged from -0.329 to 0.229. We conclude that the Greek black pig, despite its low population size, has a high degree of genetic variability, which will be useful for breeding programs aimed at maintaining long-term survival of this ancient breed. PMID:24782089

Michailidou, S; Kalivas, A; Ganopoulos, I; Stea, E; Michailidis, G; Tsaftaris, A; Argiriou, A

2014-01-01

325

Chromosome 15q25.1 genetic markers associated with level of response to alcohol in humans  

PubMed Central

As with other genetically complex common psychiatric and medical conditions, multiple genetic and environmental components contribute to alcohol use disorders (AUDs), which can confound attempts to identify genetic components. Intermediate phenotypes are often more closely correlated with underlying biology and have often proven invaluable in genetic studies. Level of response (LR) to alcohol is an intermediate phenotype for AUDs, and individuals with a low LR are at increased risk. A high rate of concurrent alcohol and nicotine use and dependence suggests that these conditions may share biochemical and genetic mechanisms. Genetic association studies indicate that a genetic locus, which includes the CHRNA5-CHRNA3-CHRNB4 gene cluster, plays a role in nicotine consumption and dependence. Genetic association with alcohol dependence was also recently shown. We show here that two of the markers from the nicotine studies also show an association (multiple testing corrected P < 0.025) with several LR phenotypes in a sample of 367 siblings. Additional markers in the region were analyzed and shown to be located in a 250-kb expanse of high linkage disequilibrium containing three additional genes. These findings indicate that LR intermediate phenotypes have utility in genetic approaches to AUDs and will prove valuable in the identification of other genetic loci conferring susceptibility to AUDs.

Joslyn, Geoff; Brush, Gerry; Robertson, Margaret; Smith, Tom L.; Kalmijn, Jelger; Schuckit, Marc; White, Raymond L.

2008-01-01

326

Chromosome 15q25.1 genetic markers associated with level of response to alcohol in humans.  

PubMed

As with other genetically complex common psychiatric and medical conditions, multiple genetic and environmental components contribute to alcohol use disorders (AUDs), which can confound attempts to identify genetic components. Intermediate phenotypes are often more closely correlated with underlying biology and have often proven invaluable in genetic studies. Level of response (LR) to alcohol is an intermediate phenotype for AUDs, and individuals with a low LR are at increased risk. A high rate of concurrent alcohol and nicotine use and dependence suggests that these conditions may share biochemical and genetic mechanisms. Genetic association studies indicate that a genetic locus, which includes the CHRNA5-CHRNA3-CHRNB4 gene cluster, plays a role in nicotine consumption and dependence. Genetic association with alcohol dependence was also recently shown. We show here that two of the markers from the nicotine studies also show an association (multiple testing corrected P < 0.025) with several LR phenotypes in a sample of 367 siblings. Additional markers in the region were analyzed and shown to be located in a 250-kb expanse of high linkage disequilibrium containing three additional genes. These findings indicate that LR intermediate phenotypes have utility in genetic approaches to AUDs and will prove valuable in the identification of other genetic loci conferring susceptibility to AUDs. PMID:19064933

Joslyn, Geoff; Brush, Gerry; Robertson, Margaret; Smith, Tom L; Kalmijn, Jelger; Schuckit, Marc; White, Raymond L

2008-12-23

327

Genetic analysis of a unique bacteriocin, Smb, produced by Streptococcus mutans GS5.  

PubMed

A dipeptide lantibiotic, named Smb, in Streptococcus mutans GS5 was characterized by molecular genetic approaches. The Smb biosynthesis gene locus is encoded by a 9.5-kb region of chromosomal DNA and consists of seven genes in the order smbM1, -T, -F, -M2, -G, -A, -B. This operon is not present in some other strains of S. mutans, including strain UA159. The genes encoding Smb were identified as smbA and smbB. Inactivation of smbM1, smbA, or smbB attenuated the inhibition of the growth of the indicator strain RP66, confirming an essential role for these genes in Smb expression. Mature Smb likely consists of the 30-amino-acid SmbA together with the 32-amino-acid SmbB. SmbA exhibited similarity with the mature lantibiotic lacticinA2 from Lactococcus lactis, while SmbB was similar to the mersacidin-like peptides from Bacillus halodurans and L. lactis. We also demonstrated that Smb expression is induced by the competence-stimulating peptide (CSP) and that a com box-like sequence is located in the smb promoter region. These results suggest that Smb belongs to the class I bacteriocin family, and its expression is dependent on CSP-induced quorum sensing. PMID:15673730

Yonezawa, Hideo; Kuramitsu, Howard K

2005-02-01

328

RFLP markers show genetic recombination in Botryotinia fuckeliana (Botrytis cinerea) and transposable elements reveal two sympatric species.  

PubMed

Molecular markers revealed that Botryotinia fuckeliana (the teleomorph of Botrytis cinerea), a haploid, filamentous, heterothallic ascomycete, contained a large amount of intrapopulation genetic variation. The markers were used to determine the mode of reproduction and the population structure of this fungus. We did not detect any differentiation between isolates from different organs, collection dates, varieties of grape, or locations in the Champagne region of France, but two unexpected sympatric populations were identified. One group of isolates (transposa) contained the transposable elements Boty and Flipper; the other (vacuma) did not. These groups differed from one another for all the other markers. RFLP markers showed that there was genetic recombination in both groups of isolates. We conclude that there are two sympatric populations of B. fuckeliana in Champagne. One species (transposa) seems to be local and well adapted, while the other one (vacuma) is presumably a heterogeneous migrant population. PMID:9364775

Giraud, T; Fortini, D; Levis, C; Leroux, P; Brygoo, Y

1997-11-01

329

A female with complete lack of Müllerian fusion, postaxial polydactyly, and tetralogy of fallot: genetic heterogeneity of McKusick-Kaufman syndrome or a unique syndrome?  

PubMed

We report a 19-year-old, non-Amish Caucasian female patient with primary amenorrhea caused by complete lack of Müllerian fusion with vaginal agenesis or Müllerian aplasia (MA), postaxial polydactyly (PAP), and tetralogy of Fallot. The genital tract anomaly of MA with and without renal or skeletal anomalies comprises Mayer-Rokitansky-Kuster-Hauser syndrome, which has not been reported with tetralogy of Fallot. The phenotypic triad of anomalies most closely resembled McKusick-Kaufman syndrome (MKS; OMIM 236700), a rare multiple congenital anomaly syndrome comprised of hydrometrocolpos (HMC), PAP, and congenital heart malformation that is inherited in an autosomal recessive pattern. While upper reproductive tract anomalies have not been reported with MKS, they have been reported with Bardet-Biedl syndrome (BBS), a syndrome that significantly overlaps with MKS. Both MKS and BBS can be caused by mutations in the MKKS or BBS6 gene on chromosome 20p12 and BBS is also associated with mutations in other genes (BBS1, BBS2, BBS4, and BBS7). To address this heterogenity, we sequenced the causative genes in MKS and BBS but no mutations in these five genes were identified. Fluorescence in situ hybridization (FISH) excluded large deletions of chromosome 20p12 and microsatellite marker studies confirmed biparental inheritance for all of the known BBS loci. The dual midline fusion defects of tetralogy of Fallot and MA suggests that either this patient has a unique syndrome with a distinct genetic etiology or that she has a genetically heterogeneous or variant form of MKS. PMID:15266619

Slavotinek, Anne M; Dutra, Amalia; Kpodzo, Dzifa; Pak, Evgenia; Nakane, Takaya; Turner, Joyce; Whiteford, Margo; Biesecker, Leslie G; Stratton, Pamela

2004-08-15

330

Determination of genetic relationships between evergreen azalea cultivars in China using AFLP markers*  

PubMed Central

Evergreen azaleas are among the most important ornamental shrubs in China. Today, there are probably over 300 cultivars preserved in different nurseries, but with little information available on the cultivar itself or relationships between cultivars. Amplified fragment length polymorphism (AFLP) markers were employed to determine the genetic relationships between evergreen azalea cultivars in China. One hundred and thirty genotypes collected from gardens and nurseries, including cultivars classified in the groups East, West, Hairy, and Summer, unknown cultivars, and close species, were analyzed using three primer pairs. A total of 408 polymorphic fragments were generated by AFLP reactions with an average of 136 fragments per primer pair. The average values of expected heterozygosity and Shannon’s information index were 0.3395 and 0.5153, respectively. Genetic similarities were generated based on Dice coefficients, used to construct a neighbor joining tree, and bootstrapped for 100 replicates in Treecon V1.3b. Principal coordinate analysis (PCO) was performed based on Dice distances using NTSYS-pc software. The AFLP technique was useful for analyzing genetic diversity in evergreen azaleas. Cluster analysis revealed that cultivars in the West and Summer groups were quite distinct from other groups in the four-group classification system and that the East and Hairy groups should be redefined.

Zhou, Hong; Liao, Jin; Xia, Yi-ping; Teng, Yuan-wen

2013-01-01

331

Novel tests for marker-disease association using the Collaborative Study on the Genetics of Alcoholism data.  

PubMed

We applied several novel tests for association and linkage in the presence of association to the Genetic Analysis Workshop 11 Problem 1 data set. Our analyses included a Hardy-Weinberg test for association between a marker and a disease susceptibility locus, a Bayesian transmission/disequilibrium test, and a Bayesian case-control test. Positive results for each of these methods require the presence of population association between the marker and a disease susceptibility locus. PMID:10597447

Nielsen, D; Zaykin, D

1999-01-01

332

An integrated genetic and cytogenetic map for the Mediterranean fruit fly, Ceratitis capitata , based on microsatellite and morphological markers  

Microsoft Academic Search

A genetic map based on microsatellite polymorphisms and visible mutations of the Mediterranean fruit fly (medfly), Ceratitis capitata is presented. Genotyping was performed on single flies from several backcross families. The map is composed of 67 microsatellites\\u000a and 16 visible markers distributed over four linkage groups. Fluorescence in situ hybridization of selected microsatellite\\u000a markers on salivary gland polytene chromosomes allowed the

Elias E. Stratikopoulos; Antonios A. Augustinos; Yannis G. Petalas; Michael N. Vrahatis; Anastasios Mintzas; Konstantinos D. Mathiopoulos; Antigone Zacharopoulou

2008-01-01

333

A Dense Genetic Map of the Silkworm, Bombyx mori, Covering All Chromosomes Based on 1018 Molecular Markers  

Microsoft Academic Search

A dense linkage map was constructed for the silkworm, Bombyx mori, containing 1018 genetic markers on all 27 autosomes and the Z chromosome. Most of the markers, covering z2000 cM, were randomly amplified polymorphic DNAs amplified with primer-pairs in combinations of 140 commercially available decanucleotides. In addition, eight known genes and five visible mutations were mapped. Bombyx homo- logues of

Yuji Yasukochi

334

Compatibility of pedigree-based and marker-based relationship matrices for single-step genetic evaluation  

PubMed Central

Background Single-step methods provide a coherent and conceptually simple approach to incorporate genomic information into genetic evaluations. An issue with single-step methods is compatibility between the marker-based relationship matrix for genotyped animals and the pedigree-based relationship matrix. Therefore, it is necessary to adjust the marker-based relationship matrix to the pedigree-based relationship matrix. Moreover, with data from routine evaluations, this adjustment should in principle be based on both observed marker genotypes and observed phenotypes, but until now this has been overlooked. In this paper, I propose a new method to address this issue by 1) adjusting the pedigree-based relationship matrix to be compatible with the marker-based relationship matrix instead of the reverse and 2) extending the single-step genetic evaluation using a joint likelihood of observed phenotypes and observed marker genotypes. The performance of this method is then evaluated using two simulated datasets. Results The method derived here is a single-step method in which the marker-based relationship matrix is constructed assuming all allele frequencies equal to 0.5 and the pedigree-based relationship matrix is constructed using the unusual assumption that animals in the base population are related and inbred with a relationship coefficient ? and an inbreeding coefficient ??/?2. Taken together, this ? parameter and a parameter that scales the marker-based relationship matrix can handle the issue of compatibility between marker-based and pedigree-based relationship matrices. The full log-likelihood function used for parameter inference contains two terms. The first term is the REML-log-likelihood for the phenotypes conditional on the observed marker genotypes, whereas the second term is the log-likelihood for the observed marker genotypes. Analyses of the two simulated datasets with this new method showed that 1) the parameters involved in adjusting marker-based and pedigree-based relationship matrices can depend on both observed phenotypes and observed marker genotypes and 2) a strong association between these two parameters exists. Finally, this method performed at least as well as a method based on adjusting the marker-based relationship matrix. Conclusions Using the full log-likelihood and adjusting the pedigree-based relationship matrix to be compatible with the marker-based relationship matrix provides a new and interesting approach to handle the issue of compatibility between the two matrices in single-step genetic evaluation.

2012-01-01

335

Genetic diversity and geographical differentiation of Iranian landrace, cultivars, and exotic chickpea lines as revealed by morphological and microsatellite markers.  

PubMed

Assessment of the extent of genetic variability within chickpea is fundamental for chickpea breeding and conservation of genetic resources and is particularly useful as a general guide in the choice of parents for breeding hybrids. To establish genetic diversity among 60 accessions of chickpea comprising landraces, internationally developed improved lines, and cultivars, genetic distances were evaluated using 14 simple sequence repeat markers. These markers showed a high level of polymorphism; a total of 59 different alleles were detected, with a mean of 4.2 alleles per locus. The polymorphic information content (PIC) value ranged from 0.31 to 0.89. All the markers, with the exception of TAA170, TA110, GA34, and Ts35, were considered to be informative (PIC?>?0.5), indicating their potential usefulness for cultivar identification. Based on the UNJ clustering method, all accessions were clustered in five groups, which indicated the probable origin and region similarity of Iranian landraces over the other cultivars. It also represents a wide diversity among available germplasm. The result has firmly established that introduction of genetic materials from exotic sources has broadened the genetic base of the national chickpea breeding program. As further implications of the findings, this study can be useful for selective breeding for specific traits and in enhancing the genetic base of breeding programs. PMID:24757326

Ghaffari, Parvin; Talebi, Reza; Keshavarzi, Fatemeh

2014-04-01

336

Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties  

PubMed Central

Simple sequence repeat (SSR) and Single Nucleotide Polymorphic (SNP), the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR) and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC) values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA) indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA) with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived ?k was plotted against the K to determine the number of populations. In case of SSR maximum ?k was at K=5 whereas, in case of SNP maximum ?k was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis.

Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R. K.; Singh, N. K.; Singh, Rakesh

2013-01-01

337

New STS molecular markers for assessment of genetic diversity and DNA fingerprinting in hop (Humulus lupulus L.).  

PubMed

Molecular markers have been increasingly used in genetic studies of crop species for their applicability in breeding programs. In this work, we report on the development of new sequence-tagged site (STS) markers based on sequence information from several identified hop (Humulus lupulus L.) genes. We demonstrate the usefulness of these STS markers and compare them to SSRs for identifying hop genotypes and estimating genetic diversity in a collection of 68 hop cultivars from around the world. We found 3 individual gene variants (A, B, C) of the chs_H1 gene in this collection. The most frequent gene variant, B (AJ304877), was not detected in Mt. Hood, Glacier, and Horizon (US) cultivars. Gene variant A came from an American germplasm through wild hops. We found length polymorphism in intron 1 of the chs2 gene, and 4 different amplified markers were detected in PCRs. The chs3 gene was found in only one third of the cultivars. None of the variants of the studied CHS genes were found in Humulus japonicus. We detected 5 major gene variants of DNA-binding protein in the collection of H. lupulus cultivars and 2 others in H. japonicus. We also found 3 individual gene variants of an endochitinase gene. The distribution of gene variants did not correlate with any resistance. We proved that developed STS markers can be successfully used for the analysis of genetic diversity and can substitute and supplement SSR markers in hop. PMID:17546067

Patzak, Josef; Vrba, Lukás; Matousek, Jaroslav

2007-01-01

338

Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers  

PubMed Central

Background Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. Results We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. Conclusions This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

2012-01-01

339

Genetic variation in a wild population of the 'sleep' passion fruit (Passiflora setacea) based on molecular markers.  

PubMed

Little is known about the molecular genetic diversity of most Passiflora species. We used RAPD markers to evaluate the genetic diversity of 24 genotypes of the 'sleep' passion fruit (Passiflora setacea). Twelve primers generated 95 markers, 88% of which were polymorphic. The genetic distance estimated by the complement of the Dice index ranged from 0.29 (among accessions Ps-G1 and Ps-G13) to 0.69 (among accessions Ps-G21 and Ps-G23). Genotype grouping based on the UPGMA algorithm showed considerable variability among genotypes. We conclude that P. setacea has a broad genetic base that could be exploited in breeding programs. PMID:22576831

Cerqueira-Silva, C B M; Santos, E S L; Conceição, L D H C S; Cardoso-Silva, C B; Pereira, A S; Oliveira, A C; Corrêa, R X

2012-01-01

340

Genetic make up and structure of Colombian populations by means of uniparental and biparental DNA markers.  

PubMed

Colombia is a country with great geographic heterogeneity and marked regional differences in pre-Columbian native population density and in the extent of past African and European immigration. As a result, Colombia has one of the most diverse populations in Latin America. Here we evaluated ancestry in over 1,700 individuals from 24 Colombian populations using biparental (autosomal and X-Chromosome), maternal (mtDNA), and paternal (Y-chromosome) markers. Autosomal ancestry varies markedly both within and between regions, confirming the great genetic diversity of the Colombian population. The X-chromosome, mtDNA, and Y-chromosome data indicate that there is a pattern across regions indicative of admixture involving predominantly Native American women and European and African men. PMID:20734436

Rojas, Winston; Parra, María Victoria; Campo, Omer; Caro, María Antonieta; Lopera, Juan Guillermo; Arias, William; Duque, Constanza; Naranjo, Andrés; García, Jharley; Vergara, Candelaria; Lopera, Jaime; Hernandez, Erick; Valencia, Ana; Caicedo, Yuri; Cuartas, Mauricio; Gutiérrez, Javier; López, Sergio; Ruiz-Linares, Andrés; Bedoya, Gabriel

2010-09-01

341

Establishment and genetic characterization of six unique tumor cell lines as preclinical models for sinonasal squamous cell carcinoma  

PubMed Central

Sinonasal squamous cell carcinomas (SCC) are rare tumors, etiologically related to occupational exposure to wood and leather dust. In spite of surgical and radiotherapeutic advances, the 5 year survival is still 30–50%. Therefore, alternative treatment options are needed. We report the establishment and characterization of six unique human sinonasal SCC cell lines, named SCCNC1, 2, 4, 5, 6 and 7. In vitro growth and invasion characteristics were evaluated and genetic profiles were compared to those of the original primary tumors. The population doubling times ranged from 21 to 34?hours. Cell lines SCCNC2 and 7 were highly invasive in matrigel. Five cell lines carried a high number of copy number alterations, including amplifications and homozygous deletions, while one showed only three abnormalities. Sequence analysis revealed three cell lines with TP53 mutation and none with KRAS or BRAF. Overexpression of p53 was observed in five, and of EGFR in four cell lines. None of the cell lines showed strong immunopositivity of p16 or presence of human papilloma virus. In conclusion, we have created six new cell lines that are clinically and genetically representative of sinonasal SCC and that will be a useful tool for the preclinical testing of new therapeutic agents.

Garcia-Inclan, Cristina; Lopez-Hernandez, Alejandro; Alonso-Guervos, Marta; Allonca, Eva; Potes, Sira; Melon, Santiago; Lopez, Fernando; Llorente, Jose Luis; Hermsen, Mario

2014-01-01

342

Establishment and genetic characterization of six unique tumor cell lines as preclinical models for sinonasal squamous cell carcinoma.  

PubMed

Sinonasal squamous cell carcinomas (SCC) are rare tumors, etiologically related to occupational exposure to wood and leather dust. In spite of surgical and radiotherapeutic advances, the 5 year survival is still 30-50%. Therefore, alternative treatment options are needed. We report the establishment and characterization of six unique human sinonasal SCC cell lines, named SCCNC1, 2, 4, 5, 6 and 7. In vitro growth and invasion characteristics were evaluated and genetic profiles were compared to those of the original primary tumors. The population doubling times ranged from 21 to 34?hours. Cell lines SCCNC2 and 7 were highly invasive in matrigel. Five cell lines carried a high number of copy number alterations, including amplifications and homozygous deletions, while one showed only three abnormalities. Sequence analysis revealed three cell lines with TP53 mutation and none with KRAS or BRAF. Overexpression of p53 was observed in five, and of EGFR in four cell lines. None of the cell lines showed strong immunopositivity of p16 or presence of human papilloma virus. In conclusion, we have created six new cell lines that are clinically and genetically representative of sinonasal SCC and that will be a useful tool for the preclinical testing of new therapeutic agents. PMID:24816148

García-Inclán, Cristina; López-Hernández, Alejandro; Alonso-Guervós, Marta; Allonca, Eva; Potes, Sira; Melón, Santiago; López, Fernando; Llorente, José Luis; Hermsen, Mario

2014-01-01

343

Population Genetic Structure in Apricot ( Prunus armeniaca L.) Cultivars Revealed by Fluorescent-AFLP Markers in Southern Xinjiang, China  

Microsoft Academic Search

Population-wide genetic structure was studied using fluorescent-AFLP markers on 85 apricot (Prunus armeniaca L.) cultivars collected from Kuche, Kashi, Hetian in the Tarim Basin, southern Xinjiang Uygur Autonomous Region of China. The purpose of this study was to determine the genetic structure and genotypic diversity among the different eco-geographical populations. Based on the results from this study, 8 pairs of

Zhaohe Yuan; Xuesen Chen; Tianming He; Jianrong Feng; Tao Feng; Chunyu Zhang

2007-01-01

344

Evaluation of genetic diversity in Turkish melons ( Cucumis melo L.) based on phenotypic characters and RAPD markers  

Microsoft Academic Search

The genetic relationships among 56 melon (Cucumis melo L.) genotypes collected from various parts of Turkey were determined by comparing their phenotypic and molecular traits with\\u000a those of 23 local and foreign melon genotypes to investigate the taxonomic relationships and genetic variation of Turkish\\u000a melon germplasm. Sixty-one phenotypic characters and 109 polymorphic RAPD markers obtained from 33 primers were used

Suat Sensoy; Saadet Büyükalaca; Kazim Abak

2007-01-01

345

Crystal structure of human esterase D: a potential genetic marker of retinoblastoma  

SciTech Connect

Retinoblastoma (RB), a carcinoma of the retina, is caused by mutations in the long arm of chromosome 13, band 13q14. The esterase D (ESD) gene maps at a similar location as the RB gene locus and therefore serves as a potential marker for the prognosis of retinoblastoma. Because very little is known about the structure and function of ESD, we determined the 3-dimensional structure of the enzyme at 1.5 {angstrom} resolution using X-ray crystallography. ESD shows a single domain with an {alpha}/{beta}-hydrolase fold. A number of insertions are observed in the canonical {alpha}/{beta}-hydrolase fold. The active site is located in a positively charged, shallow cleft on the surface lined by a number of aromatic residues. Superimposition studies helped identify the typical catalytic triad residues -- Ser-153, His264, and Asp230 -- involved in catalysis. Mutagenesis of any of the catalytic triad residues to alanine abolished the enzyme activity. Backbone amides of Leu54 and Met150 are involved in the formation of the oxyanion hole. Interestingly, a M150A mutation increased the enzyme activity by 62%. The structure of human ESD determined in this study will aid the elucidation of the physiological role of the enzyme in the human body and will assist in the early diagnosis of retinoblastoma. Wu, D., Li, Y., Song, G., Zhang, D., Shaw, N., Liu, Z. J. Crystal structure of human esterase D: a potential genetic marker of retinoblastoma.

Wu, Dong; Li, Yang; Song, Gaojie; Zhang, David; Shaw, Neil; Liu, Zhi-Jie; (Chinese Aca. Sci.)

2009-07-10

346

Resistance to Tellurite as a Selection Marker for Genetic Manipulations of Pseudomonas Strains  

PubMed Central

Resistance to the toxic compound potassium tellurite (Telr) has been employed as a selection marker built into a set of transposon vectors and broad-host-range plasmids tailored for genetic manipulations of Pseudomonas strains potentially destined for environmental release. In this study, the activated Telr determinants encoded by the cryptic telAB genes of plasmid RK2 were produced, along with the associated kilA gene, as DNA cassettes compatible with cognate vectors. In one case, the Telr determinants were assembled between the I and O ends of a suicide delivery vector for mini-Tn5 transposons. In another case, the kilA and telAB genes were combined with a minimal replicon derived from a variant of Pseudomonas plasmid pPS10, which is able to replicate in a variety of gram-negative hosts and is endowed with a modular collection of cloning and expression assets. Either in the plasmid or in the transposon vector, the Telr marker was combined with a 12-kb DNA segment of plasmid pWW0 of Pseudomonas putida mt-2 encoding the upper TOL pathway enzymes. This allowed construction of antibiotic resistance-free but selectable P. putida strains with the ability to grow on toluene as the sole carbon source through an ortho-cleavage catabolic pathway.

Sanchez-Romero, Juan M.; Diaz-Orejas, Ramon; De Lorenzo, Victor

1998-01-01

347

SIRP? and FHOD1 are unique markers of littoral cells, a recently evolved major cell population of red pulp of human spleen  

PubMed Central

Asplenic individuals are compromised not only in their ability to destroy infectious agents, but are at increased risk of death from autoimmune disease, certain tumors, and ischemic heart disease. Enhanced mortality is attributed to lack of phagocytes sequestered in spleen that efficiently engulf and destroy appropriate targets, though related cells are found elsewhere. To determine whether a unique population regulates RBC-pathogen clearance and filtration of altered self, we reviewed the anatomic literature and analyzed in situ by immunohistochemistry and immunofluorescence the expression patterns of a little-characterized cell that dominates the splenic red pulp of man and closely related primates-the venous sinus lining or littoral cell (LC). High expression of the formin FHOD1 outlines the LC population. Though LCs are endothelial-like in distribution they express several macrophage directed proteins, the RBC antigen DARC and T-cell co-receptor CD8?/? yet they lack lineage-associated markers CD34 and CD45. Strikingly, SIRP? (CD172a) expression in human spleen concentrates on LCs, consistent with recent demonstration of a key role in RBC turnover and elimination versus release of infected or altered self. Our results indicate human LCs (SIRP?+, FHOD1+, CD8?/?+, CD34?, CD45?) comprise a highly plastic barrier cell population that emerged late in primate evolution coordinate with CD8 expression. Unique to Hominidae, LCs may be the ultimate determinant of which cells re-circulate after passage through human spleen.

Ogembo, Javier Gordon; Milner, Danny A.; Mansfield, Keith G.; Rodig, Scott J.; Murphy, George F.; Kutok, Jeffery L.; Pinkus, Geraldine S.; Fingeroth, Joyce D.

2012-01-01

348

Genetic Linkage Maps of Eucalyptus Grandis and Eucalyptus Urophylla Using a Pseudo-Testcross: Mapping Strategy and Rapd Markers  

PubMed Central

We have used a ``two-way pseudo-testcross'' mapping strategy in combination with the random amplified polymorhic DNA (RAPD) assay to construct two moderate density genetic linkage maps for species of Eucalyptus. In the cross between two heterozygous individuals many single-dose RAPD markers will be heterozygous in one parent, null in the other and therefore segregate 1:1 in their F(1) progeny following a testcross configuration. Meiosis and gametic segregation in each individual can be directly and efficiently analyzed using RAPD markers. We screened 305 primers of arbitrary sequence, and selected 151 to amplify a total of 558 markers. These markers were grouped at LOD 5.0, ? = 0.25, resulting in the maternal Eucalyptus grandis map having a total of 240 markers into 14 linkage groups (1552 cM) and the paternal Eucalyptus urophylla map with 251 markers in 11 linkage groups (1101 cM) (n = 11 in Eucalyptus). Framework maps ordered with a likelihood support >/=1000:1 were assembled covering 95% of the estimated genome size in both individuals. Characterization of genome complexity of a sample of 48 mapped random amplified polymorphic DNA (RAPD) markers indicate that 53% amplify from low copy regions. These are the first reported high coverage linkage maps for any species of Eucalyptus and among the first for any hardwood tree species. We propose the combined use of RAPD markers and the pseudo-testcross configuration as a general strategy for the construction of single individual genetic linkage maps in outbred forest trees as well as in any highly heterozygous sexually reproducing living organism. A survey of the occurrence of RAPD markers in different individuals suggests that the pseudo-testcross/RAPD mapping strategy should also be efficient at the intraspecific level and increasingly so with crosses of genetically divergent individuals. The ability to quickly construct single-tree genetic linkage maps in any forest species opens the way for a shift from the paradigm of a species index map to the heterodox proposal of constructing several maps for individual trees of a population, therefore mitigating the problem of linkage equilibrium between marker and trait loci for the application of marker assisted strategies in tree breeding.

Grattapaglia, D.; Sederoff, R.

1994-01-01

349

Genetic diversity of Plasmodium vivax clinical isolates from southern Pakistan using pvcsp and pvmsp1 genetic markers  

PubMed Central

Background Plasmodium vivax is the prevalent malarial species accounting for 70% of malaria burden in Pakistan; however, there is no baseline data on the circulating genotypes. Studies have shown that polymorphic loci of gene encoding antigens pvcsp and pvmsp1 can be used reliably for conducting molecular epidemiological studies. Therefore, this study aimed to bridge the existing knowledge gap on population structure on P. vivax from Pakistan using these two polymorphic genes. Methods During the period January 2008 to May 2009, a total of 250 blood samples were collected from patients tested slide positive for P. vivax, at the Aga Khan University Hospital, Karachi, or its collection units located in Baluchistan and Sindh Province. Nested PCR/RFLP was performed, using pvcsp and pvmsp1 markers to detect the extent of genetic diversity in clinical isolates of P. vivax from southern Pakistan. Results A total of 227/250 (91%) isolates were included in the analysis while the remainder were excluded due to negative PCR outcome for P.vivax. Pvcsp analysis showed that both VK 210 (85.5%, 194/227) and VK 247 type (14.5%, 33/227) were found to be circulating in P. vivax isolates from southern Pakistan. A total of sixteen and eighty-seven genotypes of pvcsp and pvmsp-1 were detected respectively. Conclusion This is the first report from southern Pakistan on characterization of P. vivax isolates confirming that extensively diverse pvcsp and pvmsp1 variants are present within this region. Results from this study provide valuable data on genetic diversity of P. vivax that will be helpful for further epidemiological studies.

2013-01-01

350

Genetic Introgression and Species Boundary of Two Geographically Overlapping Pine Species Revealed by Molecular Markers  

PubMed Central

Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids.

Dai, Xiaogang; Xu, Jin; Li, Shuxian; Yin, Tongming

2014-01-01

351

Genetic neighbourhood of clone structures in eelgrass meadows quantified by spatial autocorrelation of microsatellite markers.  

PubMed

Limited dispersal distances in plant populations frequently cause local genetic structure, which can be quantified by spatial autocorrelation. In clonal plants, three levels of spatial organization can contribute to positive autocorrelation; namely, the neighbourhood of (a) ramets, (b) clone fragments and (c) entire clones. Here we use data from an exhaustive sampling scheme on a clonal plant to measure the contribution of the neighbourhoods of each distinct clonal structure to total spatial autocorrelation. Four plots (256 grid points each) within dense meadows of the marine clonal plant Zostera marina (eelgrass) were sampled for clone structure with nine microsatellite markers ( approximately 80 alleles). We found significant coancestry (f(ij)), at all three levels of spatial organization, even when not allowing for joins between samples of identical genets. In addition, absolute values of f(ij) and the maximum distance with significant positive f(ij) decreased with the progressive exclusion of joins between alike genotypes. The neighbourhood of this clonal plant thus consists of three levels of organization, which are reflected in different kinship structures. Each of these kinship structures may affect the level of biparental inbreeding and the physical distance between flowering shoots and their outcrossing neighbourhood. These results also emphasize the notion that spatial autocorrelation crucially depends on the scale and intensity of sampling. PMID:14576737

Hämmerli, A; Reusch, T B H

2003-11-01

352

Detection of genetic markers related to high pathogenicity in influenza by SERS.  

PubMed

We have developed a method for the detection of genetic markers associated with high pathogenicity in influenza. The assay consists of an array of 5'-thiolated ssDNA oligonucleotides immobilized on the surface of a Ag nanorod substrate that serve as capture probes for the detection of synthetic RNA sequences coding for a genetic mutation in the influenza PB1-F2 protein. Hybridization of the DNA probes to their complementary RNA sequences was detected using surface-enhanced Raman spectroscopy (SERS). Multivariate statistical analysis was used to differentiate the spectra of the complementary DNA probe-RNA target hybrids from those of the non-complementary DNA probes containing a single base pair polymorphism. Hierarchical cluster analysis (HCA) was able to distinguish with 100% accuracy the spectra of the complementary DNA probe-RNA target from the spectra of the immobilized DNA probes alone, or the DNA probes incubated with non-complementary RNA sequences. Linearity of response and limits of sensitivity of the SERS-based assays were determined using a partial least squares (PLS) regression model; detection limits computed by PLS was determined to be ~10 nM. The binding affinity of the DNA probes to their complementary RNA sequences was confirmed using enzyme-linked immunosorbent assay (ELISA); however, the detection limits observed using ELISA were approximately 10× higher (~100 nM) than those determined by PLS analysis of the SERS spectra. PMID:23833767

Negri, Pierre; Dluhy, Richard A

2013-09-01

353

Population genetic structure and trait associations in forest savory using molecular, morphological and phytochemical markers.  

PubMed

In this investigation, morphological, phytochemical and ISSR markers were used to estimate the relationships among and within seven populations of white savory (Satureja mutica), belonging to four provinces in Iran. The individuals were phenotypically diverse, which stamen length, corolla length, corolla diameter, calyx length, bract length, inflorescence length, calyx length and bracteole width were characteristics with the highest variation. Leaf dimensions were in significant correlation with flower and inflorescence characteristics. Chemical compounds of essential oils were found variable in various individuals and all samples were principally composed of phenolic constituents (carvacrol and/or thymol). As a consequence, the plants were classified into two major chemotypes including carvacrol and thymol. A total of 197 band positions were produced by 14 ISSR primers, of which 176 were found polymorphic with 88.91% polymorphism. ISSR genetic similarity values among individuals ranged between 0.45 and 0.94 which was indicative of a high level of genetic variation. Multiple regression analysis (MRA) revealed that phytochemical compositions as dependent variable, showed statistically significant correlation and in association with leaf and flower traits as independent variable, indicating a main role of leaf and flower on production of these compounds. Also, several ISSR fragments were found associated with some morphological traits and phytochemical compositions. The high diversity within and among populations of S. mutica according to different data systems could provide useful information for conservation and selection of cross-parents in breeding programs. PMID:24878369

Khadivi-Khub, Abdollah; Karimi, Ehsan; Hadian, Javad

2014-08-10

354

Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata  

PubMed Central

Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern and understanding which processes more importantly shaped the distribution of diversity, we have analyzed the uniparentally-inherited markers in ?900 individuals from an extensive sampling across the Italian peninsula, Sardinia and Sicily. Spatial PCAs and DAPCs revealed a sex-biased pattern indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West–South East Y-chromosome structure is found in continental Italy. Such structure is in agreement with recent archeological syntheses indicating two independent and parallel processes of Neolithisation. In addition, date estimates pinpoint the importance of the cultural and demographic events during the late Neolithic and Metal Ages. On the other hand, mitochondrial diversity is distributed more homogeneously in agreement with older population events that might be related to the presence of an Italian Refugium during the last glacial period in Europe.

Sarno, Stefania; Harmant, Christine; Useli, Antonella; Sanz, Paula; Yang-Yao, Daniele; Manry, Jeremy; Ciani, Graziella; Luiselli, Donata; Quintana-Murci, Lluis; Comas, David; Pettener, Davide

2013-01-01

355

Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata.  

PubMed

Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern and understanding which processes more importantly shaped the distribution of diversity, we have analyzed the uniparentally-inherited markers in ?900 individuals from an extensive sampling across the Italian peninsula, Sardinia and Sicily. Spatial PCAs and DAPCs revealed a sex-biased pattern indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West-South East Y-chromosome structure is found in continental Italy. Such structure is in agreement with recent archeological syntheses indicating two independent and parallel processes of Neolithisation. In addition, date estimates pinpoint the importance of the cultural and demographic events during the late Neolithic and Metal Ages. On the other hand, mitochondrial diversity is distributed more homogeneously in agreement with older population events that might be related to the presence of an Italian Refugium during the last glacial period in Europe. PMID:23734255

Boattini, Alessio; Martinez-Cruz, Begoña; Sarno, Stefania; Harmant, Christine; Useli, Antonella; Sanz, Paula; Yang-Yao, Daniele; Manry, Jeremy; Ciani, Graziella; Luiselli, Donata; Quintana-Murci, Lluis; Comas, David; Pettener, Davide

2013-01-01

356

Genetic and Clinical Markers of Elevated Liver Fat Content in Overweight and Obese Hispanic Children  

PubMed Central

Objective Genetic variation in six genes has been associated with elevated liver fat and nonalcoholic fatty liver disease in adults. We sought to determine the influence of these genes on liver fat and whether a genetic risk score (GRS) would improve upon the ability of common clinical risk factors to predict elevated liver fat content (ELF) in Hispanic children. Design and Methods 223 obese Hispanic children were genotyped for six SNPs. MRI was used to measure liver fat. A GRS was tested for association with ELF using multivariate linear regression. Predictors were assessed via ROC curves and pair-wise analysis was used to determine significance alone and combined with clinical markers. Results Only variants in PNPLA3 and APOC3 genes were associated with liver fat (p<0.001, p=0.01, respectively). Subjects with a GRS=4 had ~3-fold higher liver fat content than subjects with GRS of 0 (15.1±12.7% vs. 5.1±3.7%, p=0.03). While the addition of the GRS to a model containing BMI and liver enzymes increased ROC AUC from 0.83 to 0.85 [95% CI, 0.79-0.89], (p=0.01), it does not improve detection of ELF from a clinical perspective. Conclusions Only PNPLA3 and APOC3 were related to ELF and a GRS comprised of these susceptibility alleles did not add to the discriminatory power of traditional biomarkers for clinical assessment of liver fat.

Walker, Ryan W.; Sinatra, Frank; Hartiala, Jaana; Weigensberg, Marc; Spruijt-Metz, Donna; Alderete, Tanya L.; Goran, Michael I.; Allayee, Hooman

2013-01-01

357

Unexpected Genetic Diversity among and within Populations of the Toxic Dinoflagellate Alexandrium catenella as Revealed by Nuclear Microsatellite Markers?  

PubMed Central

Since 1998, blooms of Alexandrium catenella associated with paralytic shellfish poisoning have been repeatedly reported for Thau Lagoon (French Mediterranean coast). Based on data obtained for rRNA gene markers, it has been suggested that the strains involved could be closely related to the Japanese temperate Asian ribotype of the temperate Asian clade. In order to gain more insight into the origin of these organisms, we carried out a genetic analysis of 61 Mediterranean and 23 Japanese strains using both ribosomal and microsatellite markers. Whereas the phylogeny based on ribosomal markers tended to confirm the previous findings, the analysis of microsatellite sequences revealed an unexpected distinction between the French and Japanese populations. This analysis also highlighted great intraspecific diversity that was not detected with the classical rRNA gene markers. The Japanese strains are divided into two differentiated A. catenella lineages: the Sea of Japan lineage and the east coast lineage, which includes populations from the Inland Sea and the Pacific Ocean. A. catenella strains isolated from Thau Lagoon belong to another lineage. These findings indicate that microsatellite markers are probably better suited to investigations of the population genetics of this species that is distributed worldwide. Finally, application of the population genetics concepts available for macroorganisms could support new paradigms for speciation and migration in phytoplankton assemblages.

Masseret, Estelle; Grzebyk, Daniel; Nagai, Satoshi; Genovesi, Benjamin; Lasserre, Bernard; Laabir, Mohamed; Collos, Yves; Vaquer, Andre; Berrebi, Patrick

2009-01-01

358

Development of PCR-based markers for thermosensitive genetic male sterility gene tms3(t) in rice (Oryza sativa L.).  

PubMed

Development of simple and reliable PCR-based markers is an important component of marker-aided selection (MAS) activities for agronomically important genes in rice breeding. In order to develop PCR-based markers for a rice thermosensitive genetic male sterility gene tms3(t), located on chromosome 6, the nucleotide sequences of four linked RAPD markers OPF18(2600), OPAC3(640), OPB19(750) and OPM7(550) were used to design and synthesize several pairs of specific primers for PCR amplification of the genomic DNA of both the parents IR32364TGMS (sterile) and IR68 (fertile), involved in mapping this gene. For the RAPD marker OPF 18(2600), two pairs of specific primer pair combination from different positions of the sequence resulted in generation of two codominant STS (Sequence Tagged Sites) markers. In case of markers OPAC3(640), OPB19(750) and OPAA7(550) the first two could generate dominant polymorphism, while the last one could not be successful in PCR amplification. Both the codominant STSs with primer combinations F18F/F18RM and F18FM/F18RM were found to be tightly linked to the tms3(t) gene with a genetic distance of 2.7 cM. The sizes of the different alleles in case of F18F/F18RM, F18FM/F18RM combinations were 2300 bp, 1050 bp, and 1900 bp, 1000 bp respectively. The efficiency of marker-assisted selection for this trait was estimated as 84.6%. Polymorphism survey of 12 elite rice lines, indicated that these PCR-based markers for tms3(t) can now be used in selecting TGMS plants at seeding stage in the segregating populations in environment independent of controlled temperature regime. PMID:10680295

Lang, N T; Subudhi, P K; Virmani, S S; Brar, D S; Khush, G S; Li, Z; Huang, N

1999-01-01

359

Evaluation of Genetic Markers as Instruments for Mendelian Randomization Studies on Vitamin D  

PubMed Central

Background Mendelian randomization (MR) studies use genetic variants mimicking the influence of a modifiable exposure to assess and quantify a causal association with an outcome, with an aim to avoid problems with confounding and reverse causality affecting other types of observational studies. Aim We evaluated genetic markers that index differences in 25-hydroxyvitamin D (25(OH)D) as instruments for MR studies on vitamin D. Methods and Findings We used data from up-to 6,877 participants in the 1958 British birth cohort with information on genetic markers and 25(OH)D. As potential instruments, we selected 20 single nucleotide polymorphisms (SNP) which are located in the vitamin D metabolism pathway or affect skin pigmentation/tanning, including 4 SNPs from genome-wide association (GWA) meta-analyses on 25(OH)D. We analyzed SNP associations with 25(OH)D and evaluated the use of allele scores dividing genes to those affecting 25(OH)D synthesis (DHCR7, CYP2R1) and metabolism (GC, CYP24A1, CYP27B1). In addition to the GWA SNPs, only two SNPs (CYP27B1, OCA2) showed evidence for association with 25(OH)D, with the OCA2 association abolished after lifestyle adjustment. Per allele differences varied between ?0.02 and ?0.08 nmol/L (P?0.02 for all), with a 6.1 nmol/L and a 10.2 nmol/L difference in 25(OH)D between individuals with highest compared lowest number of risk alleles in synthesis and metabolism allele scores, respectively. Individual SNPs but not allele scores showed associations with lifestyle factors. An exception was geographical region which was associated with synthesis score. Illustrative power calculations (80% power, 5% alpha) suggest that approximately 80,000 participants are required to establish a causal effect of vitamin D on blood pressure using the synthesis allele score. Conclusions Combining SNPs into allele scores provides a more powerful instrument for MR analysis than a single SNP in isolation. Population stratification and the potential for pleiotropic effects need to be considered in MR studies on vitamin D.

Whittaker, John C.; Hingorani, Aroon D.; Hypponen, Elina

2012-01-01

360

Genetic diversity in Brazilian sweet potato (Ipomoea batatas (L.) Lam., Solanales, Convolvulaceae) landraces assessed with microsatellite markers  

Microsoft Academic Search

We used simple sequence repeat (SSR) markers to investigate the genetic diversity of 78 sweet potato (Ipomoea batatas) accessions (58 landraces and 20 putative clones) from traditional agricultural households from 19 local communities in the Vale do Ribeira, São Paulo, Brazil. Eight SSR loci were assessed using 6% (w\\/v) polyacrylamide gels stained with silver nitrate and the accessions genotyped considering

Elizabeth Ann Veasey; Aline Borges; Mariana Silva Rosa; Jurema R. Queiroz-Silva; Eduardo de Andrade Bressan; Nivaldo Peroni

2008-01-01

361

Genetic analysis of Indian aromatic and quality rice ( Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers  

Microsoft Academic Search

Genetic relationships among Indian aromatic and quality rice (Oryza sativa) germplasm were assessed using 30 fluorescently labeled rice microsatellite markers. The 69 rice genotypes used in this study included 52 Basmati and other scented\\/quality rice varieties from different parts of India and 17 indica and japonica varieties that served as controls. A total of 235 alleles were detected at the

Sunita Jain; Rajinder K. Jain; Susan R. McCouch

2004-01-01

362

Estimation of genetic diversity in some Iranian wild Prunus subgenus Cerasus accessions using inter-simple sequence repeat (ISSR) markers  

Microsoft Academic Search

As Iran is one of the main origins of Prunus germplasm. In this study, ISSR markers were used for genetic diversity evaluation of 39 accessions of subgenus Cerasus belonging to six species i.e. Prunus avium L., Prunus cerasus L., Prunus mahaleb L., Prunus incana Pall., Prunus microcarpa Boiss., and Prunus brachypetala Boiss.. With 12 ISSR primers, 151 polymorphic bands were

Ali Shahi-Gharahlar; Zabihollah Zamani; Reza Fatahi; Naser Bouzari

2011-01-01

363

Genetic models to estimate additive and non-additive effects of marker-associated QTL using multiple regression techniques  

Microsoft Academic Search

The development of molecular markers has recently raised expectations for their application in selection programs. However, some questions related to quantitative trait loci (QTL) identification are still unanswered. The objectives of this paper are (1) to develop statistical genetic models for detecting and locating on the genome multi-QTL with additive, dominance and epistatic effects using multiple linear regression analysis in

J. Moreno-Gonzalez

1992-01-01

364

Genetic homogeneity of in vitro raised plants of grapevine cv. Crimson Seedless revealed by ISSR and microsatellite markers  

Microsoft Academic Search

The present study was conducted to test the clonal homogeneity of six month old tissue culture raised plants of grapevine cv. Crimson Seedless using Inter Simple Sequence Repeat (ISSR) and Simple Sequence Repeat (SSR) markers. Visible assessment of these in vitro raised plants maintained in polyhouse did not show any morphological differences among themselves. However, to test the genetic homogeneity

A. Nookaraju; D. C. Agrawal

365

Genetic linkage map of EST-SSR and SRAP markers in the endangered Chinese endemic herb Dendrobium (Orchidaceae).  

PubMed

Dendrobium officinale is an endangered orchid from southeast Asia that is known for its medicinal properties in traditional Chinese medicine. We constructed an integrated genetic linkage map of an F(1) population derived from an interspecific cross between D. officinale and D. aduncum (both, 2n = 38), using expressed sequence tag-simple sequence repeats (EST-SSR) and sequence-related amplified polymorphism (SRAP). A total of 349 polymorphic loci, including 261 SRAP loci and 88 EST-SSR loci, were identified for genetic linkage analysis. The software JoinMap 4.0 was used to construct the genetic maps. A total of 157 loci were arranged into 27 major linkage groups, each containing a minimum of four markers, and a further 23 markers were distributed to five triplets and four doublets, the frame map covered a total distance of 1580.4 cM, with a mean of 11.89 cM between adjacent markers. This primary map of the D. officinale and D. aduncum hybrid provides a basis for genetic studies and should facilitate future studies of medical traits mapping and marker-assisted selection in Dendrobium species breeding programs. PMID:23315811

Lu, J J; Wang, S; Zhao, H Y; Liu, J J; Wang, H Z

2012-01-01

366

Development of microsatellite markers for genetic diversity analysis of Dendrobium loddigesii Rolfe, an endangered orchid in China  

Microsoft Academic Search

Dendrobium loddigesii Rolfe is an endangered epiphytic orchid with high medicinal and horticulture value. To estimate genetic diversity and population structure of D. loddigesii, 12 new microsatellite markers of D. loddigesii were developed from an enriched library. A total of 98 alleles were detected with an average of 8.2 alleles per locus. The expected heterozygosity of each SSR locus varied

Xiaoyan Cai; Zhenyu Feng; Beiwei Hou; Wenrui Xing; Xiaoyu Ding

367

Genetic diversity of Ligula intestinalis (Cestoda: Diphyllobothriidea) based on analysis of inter-simple sequence repeat markers  

Microsoft Academic Search

In order to investigate the genetic diversity of Ligula intestinalis populations, nine inter-simple sequence repeat (ISSR) markers were applied to populations from nine geographical areas around the world and 10 host species. The 110 loci selected from the ISSR patterns produced revealed high variability among the analysed samples, with a polymorphism of 100% and a global coefficient of gene differentiation

W. Bouzid; S. Lek; M. Mace; O. Ben Hassine; R. Etienne; L. Legal; G. Loot

2008-01-01

368

Genetic diversity assessment in nine cultivars of Catharanthus roseus from Central Gujarat (India) through RAPD, ISSR and SSR markers  

Microsoft Academic Search

The genetic relationship study was carried out among nine different cultivars of Catharanthus roseus using RAPD, ISSR and SSR markers. In RAPD analysis, out of twenty primers, six primers amplified 592 bands out of which 466 were polymorphic while rest was monomorphic. This gave high (78.71%) polymorphism among nine cultivars. In ISSR analysis, 78.94% polymorphism was observed, while in SSR

Sanjay Lal; Kinnari N. Mistry; Smit D. Shah; Riddhi Thaker

2011-01-01

369

Comparative analyses of mitochondrial and nuclear genetic markers for the molecular identification of Rhipicephalus spp.  

PubMed

The genus Rhipicephalus (Acari: Ixodidae) comprises a large number of vectors of pathogens of substantial medical and veterinary concern; however, species identification based solely on morphological features is often challenging. In the present study, genetic distance within selected Rhipicephalus species (i.e., Rhipicephalus bursa, Rhipicephalus guilhoni, Rhipicephalus muhsamae, Rhipicephalus sanguineus sensu lato and Rhipicephalus turanicus), were investigated based on molecular and phylogenetic analyses of fragments of the mitochondrial 16S, 12S and cytochrome c oxidase subunit 1 (cox1) genes, as well as of the whole sequences of the ribosomal internal transcribed spacer-2 (ITS-2) region. Mean values of inter-specific genetic distance (e.g., up to 12.6%, 11.1% and 15.2%), as well as of intra-specific genetic distance (e.g., 0.9%, 0.9% and 1%), calculated using the Kimura-2 parameter substitution model with uniform rates among sites for 16S, 12S and cox1 genes, respectively, confirmed the differentiation of the rhipicephaline species herein examined. The molecular identification was also supported by the distinct separation of species-specific clades inferred from the phylogenetic analyses of all mitochondrial sequences. Conversely, little interspecific divergence was detected amongst ribosomal ITS-2 sequences (i.e., up to 2.8%) for species belonging to the R. sanguineus complex, which resulted in the ambiguous placement of selected R. sanguineus s.l. and R. turanicus sequences in the corresponding phylogenetic tree. Results from this study confirm the suitability of mtDNA markers for the reliable identification of ticks within the Rhipicephalus genus and provide a framework for future studies of taxonomy, speciation history and evolution of this group of ticks. PMID:24103336

Latrofa, Maria S; Dantas-Torres, Filipe; Annoscia, Giada; Cantacessi, Cinzia; Otranto, Domenico

2013-12-01

370

Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius).  

PubMed

Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (F(CT) = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (F(CT) range 0.275-0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries. PMID:24138219

Milano, Ilaria; Babbucci, Massimiliano; Cariani, Alessia; Atanassova, Miroslava; Bekkevold, Dorte; Carvalho, Gary R; Espiñeira, Montserrat; Fiorentino, Fabio; Garofalo, Germana; Geffen, Audrey J; Hansen, Jakob H; Helyar, Sarah J; Nielsen, Einar E; Ogden, Rob; Patarnello, Tomaso; Stagioni, Marco; Tinti, Fausto; Bargelloni, Luca

2014-01-01

371

Genetic variation in the Solanaceae fruit bearing species lulo and tree tomato revealed by Conserved Ortholog (COSII) markers  

PubMed Central

The Lulo or naranjilla (Solanum quitoense Lam.) and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt.) are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32) and tree tomatoes (n = 30) through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII) in other Solanaceae (Asterid) species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested) and tree tomatoes (26 out of 41) for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with FST > 0.90), which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species.

2010-01-01

372

Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?  

PubMed

Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using real and simulated molecular marker data. Our study also compared the performance of traditional hierarchical clustering with model-based clustering (STRUCTURE). We showed that the cophenetic correlation coefficient is directly related to subgroup differentiation and can thus be used as an indicator of the presence of genetically distinct subgroups in germplasm collections. Whereas UPGMA performed well in preserving distances between accessions, Ward excelled in recovering groups. Our results also showed a close similarity between clusters obtained by Ward and by STRUCTURE. Traditional cluster analysis can provide an easy and effective way of determining structure in germplasm collections using molecular marker data, and, the output can be used for sampling core collections or for association studies. PMID:21472410

Odong, T L; van Heerwaarden, J; Jansen, J; van Hintum, T J L; van Eeuwijk, F A

2011-07-01

373

Development and Characterization of a Genetic Linkage Map of Cryptococcus neoformans var. neoformans Using Amplified Fragment Length Polymorphisms and Other Markers  

Microsoft Academic Search

A segregating population of single basidiospore isolates from a sexual cross was used to generate the first moderately dense genetic linkage map of Cryptococcus neoformans var. neoformans (Serotype D). Polymorphic DNA markers were developed using amplified fragment length polymorphisms, random amplified polymorphic DNA, and gene-encoding sequences. These markers were used to analyze 100 meiotic progeny. All markers were tested for

Anja Forche; Jianping Xu; Rytas Vilgalys; Thomas G. Mitchell

2000-01-01

374

Novel Tetra-nucleotide Microsatellite DNA Markers for Assessing the Evolutionary Genetics and Demographics of Northern Snakehead (Channa argus) Invading North America  

USGS Publications Warehouse

We document the isolation and characterization of 19 tetra-nucleotide microsatellite DNA markers in northern snakehead (Channa argus) fish that recently colonized Meadow Lake, New York City, New York. These markers displayed moderate levels of allelic diversity (averaging 6.8 alleles/locus) and heterozygosity (averaging 74.2%). Demographic analyses suggested that the Meadow Lake collection has not achieved mutation-drift equilibrium. These results were consistent with instances of deviations from Hardy-Weinberg equilibrium and the presence of some linkage disequilibrium. A comparison of individual pair-wise distances suggested the presence of multiple differentiated groups of related individuals. Results of all analyses are consistent with a pattern of multiple, recent introductions. The microsatellite markers developed for C. argus yielded sufficient genetic diversity to potentially: (1) delineate kinship; (2) elucidate fine-scale population structure; (3) define management (eradication) units; (4) estimate dispersal rates; (5) estimate population sizes; and (6) provide unique demographic perspectives of control or eradication effectiveness

King, Timothy L; Johnson, R.L.

2011-01-01

375

Population genetics of 17 Y-STR markers in West Libya (Tripoli region).  

PubMed

Seventeen Y-chromosomal Short Tandem Repeats (Y-STR) included in the AmpFlSTR Y-filer PCR Amplification kit (Applied Biosystems) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4) were genotyped in a population sample of 176 unrelated males from western Libya (Tripoli region). A total of 142 different haplotypes were found, 124 being unique. Haplotype diversity was 0.9950. Both R(ST) pairwise analyses and multidimensional scaling plot show a close genetic relationship between Tripoli and North African populations. PMID:23473875

Triki-Fendri, Soumaya; Sánchez-Diz, Paula; Rey-González, Danel; Ayadi, Imen; Alfadhli, Suad; Rebai, Ahmed; Carracedo, Ángel

2013-05-01

376

Genetic differentiation induced by spaceflight treatment of Cistanche deserticola and identification of inter-simple sequence repeat markers associated with its medicinal constituent contents  

NASA Astrophysics Data System (ADS)

The dried, fleshy stems of Cistanche deserticola (Orobanchaceae) are popular tonics in Traditional Chinese Medicine (TCM) to treat the inability of kidney in expelling extra fluid in the body, causing fluid retention, and reform reproductive system. However, the wild plants of C. deserticola have become endangered due to habitat downsizing and over-harvesting for its medicinal usages. The present research was carried out for the following purposes: (1) promoting the space-breeding research; (2) providing molecular evidence for agricultural selective breeding; and (3) protecting this endangered herbal medicine and conserving its genetic resources.In this study, plants were cultivated from seeds specifically treated in spaceflight for seven days, and sampled to screen positive mutants and identify ISSR markers associated with their medicinal constituents. As a result, nine out of the 94 ISSR primers were showed high polymorphism, and a total of 118 bands were generated, of which 80 were polymorphic, ranging from 250 to 2600 bp. The spaceflight mutants were found to have lower coefficient of gene differentiation (Gst = 0.0269), and higher gene flow (Nm = 18.0740) than those of the controls (Gst = 0.2067 and Nm = 1.9185). The results demonstrated that most of the genetic variation were harnessed within populations (>97%). The Analysis of Molecular Variance (AMOVA) revealed high genetic variation within populations (88.03%) and low genetic differentiation among regions (-18.83%) and populations (30.79%), respectively. The results also indicated a profound difference between spaceflight condition and that on the earth. The unique vacuum environment of spaceflight was suggested to induce DNA mutation and various variations of C. deserticola. In addition, six particular ISSR markers were identified, cloned and sequenced; one of them, CA41939-934, was found positively correlated with acteoside with correlation coefficient values of 0.264 (P < 0.05). Our work may provide a valuable molecular evidence for establishing conservation strategies and space-breeding research program.

Wu, Y.; Yang, D. Y.; Tu, P. F.; Tian, Y. Z.; Guo, Y. H.; Wang, X. M.; Li, X. B.

2011-02-01

377

New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species  

PubMed Central

Background and Aims Lolium perenne (perennial ryegrass) is the most important forage grass species of temperate regions. We have previously released the chloroplast genome sequence of L. perenne ‘Cashel’. Here nine chloroplast microsatellite markers are published, which were designed based on knowledge about genetically variable regions within the L. perenne chloroplast genome. These markers were successfully used for characterizing the genetic diversity in Lolium and different grass species. Methods Chloroplast genomes of 14 Poaceae taxa were screened for mononucleotide microsatellite repeat regions and primers designed for their amplification from nine loci. The potential of these markers to assess genetic diversity was evaluated on a set of 16 Irish and 15 European L. perenne ecotypes, nine L. perenne cultivars, other Lolium taxa and other grass species. Key Results All analysed Poaceae chloroplast genomes contained more than 200 mononucleotide repeats (chloroplast simple sequence repeats, cpSSRs) of at least 7 bp in length, concentrated mainly in the large single copy region of the genome. Nucleotide composition varied considerably among subfamilies (with Pooideae biased towards poly A repeats). The nine new markers distinguish L. perenne from all non-Lolium taxa. TeaCpSSR28 was able to distinguish between all Lolium species and Lolium multiflorum due to an elongation of an A8 mononucleotide repeat in L. multiflorum. TeaCpSSR31 detected a considerable degree of microsatellite length variation and single nucleotide polymorphism. TeaCpSSR27 revealed variation within some L. perenne accessions due to a 44-bp indel and was hence readily detected by simple agarose gel electrophoresis. Smaller insertion/deletion events or single nucleotide polymorphisms detected by these new markers could be visualized by polyacrylamide gel electrophoresis or DNA sequencing, respectively. Conclusions The new markers are a valuable tool for plant breeding companies, seed testing agencies and the wider scientific community due to their ability to monitor genetic diversity within breeding pools, to trace maternal inheritance and to distinguish closely related species.

Diekmann, Kerstin; Hodkinson, Trevor R.; Barth, Susanne

2012-01-01

378

Application of microsatellite markers in conservation genetics and fisheries management: recent advances in population structure analysis and conservation strategies.  

PubMed

Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management. PMID:24808959

Abdul-Muneer, P M

2014-01-01

379

Identification of Nonpoint Sources of Fecal Pollution in Coastal Waters by Using Host-Specific 16S Ribosomal DNA Genetic Markers from Fecal Anaerobes  

Microsoft Academic Search

We describe a new PCR-based method for distinguishing human and cow fecal contamination in coastal waters without culturing indicator organisms, and we show that the method can be used to track bacterial marker sequences in complex environments. We identified two human-specific genetic markers and five cow-specific genetic markers in fecal samples by amplifying 16S ribosomal DNA (rDNA) fragments from members

ANNE E. BERNHARD; KATHARINE G. FIELD

2000-01-01

380

Genetic diversity of the Chinese traditional herb Blumea balsamifera (Asteraceae) based on AFLP markers.  

PubMed

Blumea balsamifera is a commercially important medicinal herb in China and other parts of Asia. It is used to produce borneol. This plant grows in the wild, but resources have diminished greatly in recent years. We examined the genetic diversity of this species to help develop conservation strategies; 35 plants from five provinces were analyzed using AFLPs. Eight AFLP primer combinations generated 1367 fragments, giving a mean of 172 fragments per primer combination. Polymorphism in the germplasm analysis was found for 1360 (99.48%) of the fragments, of which 264 (19.27%) fragments were unique (accession specific) and 423 (25.33%) of the fragments were rare (present in less than 10% of the accessions). The polymorphic fragments were used to group the accessions in a UPGMA phenogram. Most grouping was geographical. In general, accessions coming from Guizhou and Guangxi showed higher diversities as these accessions were scattered in different groups. The genetic distance estimated by Jaccard similarity coefficient index showed low variability among genotypes (coefficient value ranged from 0.60 to 0.95). More attention should be given to the study and conservation of the biodiversity of this economically important genus. PMID:24782086

Pang, Y X; Wang, W Q; Zhang, Y B; Yuan, Y; Yu, J B; Zhu, M; Chen, Y Y

2014-01-01

381

Assessment of genetic diversity in Trigonella foenum-graecum and Trigonella caerulea using ISSR and RAPD markers  

PubMed Central

Background Various species of genus Trigonella are important from medical and culinary aspect. Among these, Trigonella foenum-graecum is commonly grown as a vegetable. This anti-diabetic herb can lower blood glucose and cholesterol levels. Another species, Trigonella caerulea is used as food in the form of young seedlings. This herb is also used in cheese making. However, little is known about the genetic variation present in these species. In this report we describe the use of ISSR and RAPD markers to study genetic diversity in both, Trigonella foenum-graecum and Trigonella caerulea. Results Seventeen accessions of Trigonella foenum-graecum and nine accessions of Trigonella caerulea representing various countries were analyzed using ISSR and RAPD markers. Genetic diversity parameters (average number of alleles per polymorphic locus, percent polymorphism, average heterozygosity and marker index) were calculated for ISSR, RAPD and ISSR+RAPD approaches in both the species. Dendrograms were constructed using UPGMA algorithm based on the similarity index values for both Trigonella foenum-graecum and Trigonella caerulea. The UPGMA analysis showed that plants from different geographical regions were distributed in different groups in both the species. In Trigonella foenum-graecum accessions from Pakistan and Afghanistan were grouped together in one cluster but accessions from India and Nepal were grouped together in another cluster. However, in both the species accessions from Turkey did not group together and fell in different clusters. Conclusions Based on genetic similarity indices, higher diversity was observed in Trigonella caerulea as compared to Trigonella foenum-graecum. The genetic similarity matrices generated by ISSR and RAPD markers in both species were highly correlated (r = 0.78 at p = 0.001 for Trigonella foenum-graecum and r = 0.98 at p = 0.001 for Trigonella caerulea) indicating congruence between these two systems. Implications of these observations in the analysis of genetic diversity and in supporting the possible Center of Origin and/or Diversity for Trigonella are discussed.

Dangi, Rakhee S; Lagu, Meena D; Choudhary, Lal B; Ranjekar, Prabhakar K; Gupta, Vidya S

2004-01-01

382

Start Codon Targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl., an endangered medicinal orchid species.  

PubMed

Genetic variability in the wild genotypes of Dendrobium nobile Lindl. collected from different parts of Northeast India, was analyzed using a Start Codon Targeted (SCoT) marker system. A total of sixty individuals comprising of six natural populations were investigated for the existing natural genetic diversity. One hundred and thirty two (132) amplicons were produced by SCoT marker generating 96.21% polymorphism. The PIC value of the SCoT marker system was 0.78 and the Rp values of the primers ranged between 4.43 and 7.50. The percentage of polymorphic loci (Pp) ranging from 25% to 56.82%, Nei's gene diversity (h) from 0.08 to 0.15 with mean Nei's gene diversity of 0.28, and Shannon's information index (I) values ranging from 0.13 to 0.24 with an average value of 0.43 were recorded. The gene flow value (0.37) and the diversity among populations (0.57) demonstrated higher genetic variation among the populations. Analysis of molecular variance (AMOVA) showed 43.37% of variation within the populations, whereas 56.63% variation was recorded among the populations. Cluster analysis also reveals high genetic variation among the genotypes. Present investigation suggests the effectiveness of SCoT marker system to estimate the genetic diversity of D. nobile and that it can be seen as a preliminary point for future research on the population and evolutionary genetics of this endangered orchid species of medicinal importance. PMID:23939470

Bhattacharyya, Paromik; Kumaria, Suman; Kumar, Shrawan; Tandon, Pramod

2013-10-15

383

Genetic rearrangements of six wheat-agropyron cristatum 6P addition lines revealed by molecular markers.  

PubMed

Agropyron cristatum (L.) Gaertn. (2n?=?4x?=?28, PPPP) not only is cultivated as pasture fodder but also could provide many desirable genes for wheat improvement. It is critical to obtain common wheat-A. cristatum alien disomic addition lines to locate the desired genes on the P genome chromosomes. Comparative analysis of the homoeologous relationships between the P genome chromosome and wheat genome chromosomes is a key step in transferring different desirable genes into common wheat and producing the desired alien translocation line while compensating for the loss of wheat chromatin. In this study, six common wheat-A. cristatum disomic addition lines were produced and analyzed by phenotypic examination, genomic in situ hybridization (GISH), SSR markers from the ABD genomes and STS markers from the P genome. Comparative maps, six in total, were generated and demonstrated that all six addition lines belonged to homoeologous group 6. However, chromosome 6P had undergone obvious rearrangements in different addition lines compared with the wheat chromosome, indicating that to obtain a genetic compensating alien translocation line, one should recombine alien chromosomal r